Generated best practices file

Azure AD authentication for OpenAI services

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,38 @@
+name: "\U0001FAB2 Bug Report"
+description: Submit a bug report
+labels: ["bug"]
+body:
+
+  - type: dropdown
+    id: information-git-provider
+    attributes:
+      label: Git provider
+      description: 'The problem arises when using:'
+      options:
+        - "Github Cloud"
+        - "Github Enterprise"
+        - "Gitlab"
+        - "Bitbucket Cloud"
+        - "Bitbucket Server"
+        - "Azure"
+        - "Other"
+    validations:
+      required: true
+
+  - type: textarea
+    id: system-info
+    attributes:
+      label: System Info
+      description: Please share your system info with us.
+      placeholder: model used, deployment type (action/app/cli/...), etc...
+    validations:
+      required: true
+
+  - type: textarea
+    id: bug-details
+    attributes:
+      label: Bug details
+      description: Please describe the problem.
+      placeholder: Describe the problem
+    validations:
+      required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,10 @@
+blank_issues_enabled: false
+version: 0.1
+contact_links:
+  - name: Discussions
+    url: https://github.com/qodo-ai/pr-agent/discussions
+    about: GitHub Discussions
+
+  - name: Discord community
+    url: https://discord.com/channels/1057273017547378788/1126104260430528613
+    about: Join our discord community

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,21 @@
+name: "\U0001F4A1 Feature request"
+description: Submit a proposal/request for a new PR-Agent feature
+labels: ["feature"]
+body:
+  - type: textarea
+    id: feature-request
+    validations:
+      required: true
+    attributes:
+      label: Feature request
+      description: |
+        Description of the feature proposal.
+
+  - type: textarea
+    id: motivation
+    validations:
+      required: true
+    attributes:
+      label: Motivation
+      description: |
+        Outline the motivation for the proposal.

.github/ISSUE_TEMPLATE/miscellaneous.yml

@@ -0,0 +1,36 @@
+name: "❔ General Issue"
+description: Submit a general issue
+labels: ["general"]
+body:
+
+  - type: dropdown
+    id: information-git-provider
+    attributes:
+      label: Git provider (optional)
+      description: 'Git Provider:'
+      options:
+        - "Github Cloud"
+        - "Github Enterprise"
+        - "Gitlab"
+        - "Bitbucket Cloud"
+        - "Bitbucket Server"
+        - "Azure"
+        - "Other"
+
+  - type: textarea
+    id: system-info
+    attributes:
+      label: System Info (optional)
+      description: Please share your system info with us.
+      placeholder: model used, deployment type (action/app/cli/...), etc...
+    validations:
+      required: false
+
+  - type: textarea
+    id: issues-details
+    attributes:
+      label: Issues details
+      description: Please share the issues details.
+      placeholder: Describe the issue
+    validations:
+      required: true

.gitignore

@@ -1,6 +1,7 @@
 .idea/
 .lsp/
 .vscode/
+.env
 venv/
 pr_agent/settings/.secrets.toml
 __pycache__
@@ -9,3 +10,4 @@ dist/
 build/
 .DS_Store
 docs/.cache/
+.qodo

CODE_OF_CONDUCT.md

@@ -0,0 +1,45 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of fostering an open
+and welcoming community, we pledge to respect all people who contribute through reporting
+issues, posting feature requests, updating documentation, submitting pull requests or
+patches, and other activities.
+
+We are committed to making participation in this project a harassment-free experience for
+everyone, regardless of level of experience, gender, gender identity and expression,
+sexual orientation, disability, personal appearance, body size, race, ethnicity, age,
+religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic addresses,
+  without explicit permission
+* Other unethical or unprofessional conduct
+
+Project maintainers have the right and responsibility to remove, edit, or reject comments,
+commits, code, wiki edits, issues, and other contributions that are not aligned to this
+Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors
+that they deem inappropriate, threatening, offensive, or harmful.
+
+By adopting this Code of Conduct, project maintainers commit themselves to fairly and
+consistently applying these principles to every aspect of managing this project. Project
+maintainers who do not follow or enforce the Code of Conduct may be permanently removed
+from the project team.
+
+This Code of Conduct applies both within project spaces and in public spaces when an
+individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by
+contacting a project maintainer at tal.r@qodo.ai . All complaints will
+be reviewed and investigated and will result in a response that is deemed necessary and
+appropriate to the circumstances. Maintainers are obligated to maintain confidentiality
+with regard to the reporter of an incident.
+
+This Code of Conduct is adapted from the
+[Contributor Covenant](https://contributor-covenant.org), version 1.3.0, available at
+[contributor-covenant.org/version/1/3/0/](https://contributor-covenant.org/version/1/3/0/)
+

CONTRIBUTING.md

@@ -0,0 +1,38 @@
+# Contributing to PR-Agent
+
+Thank you for your interest in contributing to the PR-Agent project! 
+
+## Getting Started
+
+1. Fork the repository and clone your fork
+2. Install Python 3.10 or higher
+3. Install dependencies (`requirements.txt` and `requirements-dev.txt`)
+4. Create a new branch for your contribution:
+   - For new features: `git checkout -b feature/your-feature-name`
+   - For bug fixes: `git checkout -b fix/issue-description`
+5. Make your changes
+6. Write or update tests as needed
+7. Run tests locally to ensure everything passes
+8. Commit your changes using conventional commit messages
+9. Push to your fork and submit a pull request
+
+## Development Guidelines
+
+- Keep pull requests focused on a single feature or fix
+- Follow the existing code style and formatting conventions
+- Add unit tests for any new functionality using pytest
+- Ensure test coverage for your changes
+- Update documentation as needed
+
+## Pull Request Process
+
+1. Ensure your PR includes a clear description of the changes
+2. Link any related issues
+3. Update the README.md if needed
+4. Wait for review from maintainers
+
+## Questions or Need Help?
+
+- Join our [Discord community](https://discord.com/channels/1057273017547378788/1126104260430528613) for questions and discussions
+- Check the [documentation](https://qodo-merge-docs.qodo.ai/) for detailed information
+- Report bugs or request features through [GitHub Issues](https://github.com/qodo-ai/pr-agent/issues)

Dockerfile.github_action

@@ -3,7 +3,7 @@ FROM python:3.12 as base
 WORKDIR /app
 ADD pyproject.toml .
 ADD requirements.txt .
-RUN pip install . && rm pyproject.toml requirements.txt
+RUN pip install --no-cache-dir . && rm pyproject.toml requirements.txt
 ENV PYTHONPATH=/app
 ADD docs docs
 ADD pr_agent pr_agent

README.md

@@ -4,77 +4,82 @@
 
 
 <picture>
-  <source media="(prefers-color-scheme: dark)" srcset="https://codium.ai/images/pr_agent/logo-dark.png" width="330">
-  <source media="(prefers-color-scheme: light)" srcset="https://codium.ai/images/pr_agent/logo-light.png" width="330">
+  <source media="(prefers-color-scheme: dark)" srcset="https://www.qodo.ai/wp-content/uploads/2025/02/PR-Agent-Purple-2.png">
+  <source media="(prefers-color-scheme: light)" srcset="https://www.qodo.ai/wp-content/uploads/2025/02/PR-Agent-Purple-2.png">
   <img src="https://codium.ai/images/pr_agent/logo-light.png" alt="logo" width="330">
 
 </picture>
 <br/>
-Qode Merge PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedback and suggestions
+
+ [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) | 
+[Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) | 
+[Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) | 
+[Qodo Merge](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) 💎
+
+PR-Agent aims to help efficiently review and handle pull requests, by providing AI feedback and suggestions
 </div>
 
-[![Static Badge](https://img.shields.io/badge/Chrome-Extension-violet)](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl)
+[![Static Badge](https://img.shields.io/badge/Chrome-Extension-violet)](https://chromewebstore.google.com/detail/qodo-merge-ai-powered-cod/ephlnjeghhogofkifjloamocljapahnl)
 [![Static Badge](https://img.shields.io/badge/Pro-App-blue)](https://github.com/apps/qodo-merge-pro/)
 [![Static Badge](https://img.shields.io/badge/OpenSource-App-red)](https://github.com/apps/qodo-merge-pro-for-open-source/)
-[![Discord](https://badgen.net/badge/icon/discord?icon=discord&label&color=purple)](https://discord.com/channels/1057273017547378788/1126104260430528613)
+[![Discord](https://badgen.net/badge/icon/discord?icon=discord&label&color=purple)](https://discord.com/invite/SgSxuQ65GF)
 <a href="https://github.com/Codium-ai/pr-agent/commits/main">
 <img alt="GitHub" src="https://img.shields.io/github/last-commit/Codium-ai/pr-agent/main?style=for-the-badge" height="20">
 </a>
 </div>
 
-### [Documentation](https://pr-agent-docs.codium.ai/)
-- See the [Installation Guide](https://qodo-merge-docs.qodo.ai/installation/) for instructions on installing Qode Merge PR-Agent on different platforms.
+[//]: # (### [Documentation]&#40;https://qodo-merge-docs.qodo.ai/&#41;)
 
-- See the [Usage Guide](https://qodo-merge-docs.qodo.ai/usage-guide/) for instructions on running Qode Merge PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.
+[//]: # ()
+[//]: # (- See the [Installation Guide]&#40;https://qodo-merge-docs.qodo.ai/installation/&#41; for instructions on installing PR-Agent on different platforms.)
 
-- See the [Tools Guide](https://qodo-merge-docs.qodo.ai/tools/) for a detailed description of the different tools, and the available configurations for each tool.
+[//]: # ()
+[//]: # (- See the [Usage Guide]&#40;https://qodo-merge-docs.qodo.ai/usage-guide/&#41; for instructions on running PR-Agent tools via different interfaces, such as CLI, PR Comments, or by automatically triggering them when a new PR is opened.)
+
+[//]: # ()
+[//]: # (- See the [Tools Guide]&#40;https://qodo-merge-docs.qodo.ai/tools/&#41; for a detailed description of the different tools, and the available configurations for each tool.)
 
 
 ## Table of Contents
+
 - [News and Updates](#news-and-updates)
 - [Overview](#overview)
 - [Example results](#example-results)
 - [Try it now](#try-it-now)
-- [PR-Agent Pro 💎](https://pr-agent-docs.codium.ai/overview/pr_agent_pro/)
+- [Qodo Merge](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/)
 - [How it works](#how-it-works)
 - [Why use PR-Agent?](#why-use-pr-agent)
 
 ## News and Updates
 
-### December 2, 2024
+## Apr 14, 2025
 
-Open-source repositories can now freely use Qodo Merge Pro, and enjoy easy one-click installation using a marketplace [app](https://github.com/apps/qodo-merge-pro-for-open-source).
+GPT-4.1 is out. And its quite good on coding tasks...
 
-<kbd><img src="https://github.com/user-attachments/assets/b0838724-87b9-43b0-ab62-73739a3a855c" width="512"></kbd>
+https://openai.com/index/gpt-4-1/
 
-See [here](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/) for more details about installing Qodo Merge Pro for private repositories.
+<img width="635" alt="image" src="https://github.com/user-attachments/assets/a8f4c648-a058-4bdc-9825-2a4bb71a23e5" />
 
 
-### November 18, 2024
+## March 28, 2025
+A new version, v0.28, was released. See release notes [here](https://github.com/qodo-ai/pr-agent/releases/tag/v0.28).
 
-A new mode was enabled by default for code suggestions - `--pr_code_suggestions.focus_only_on_problems=true`:
+This version includes a new tool, [Help Docs](https://qodo-merge-docs.qodo.ai/tools/help_docs/), which can answer free-text questions based on a documentation folder.
 
-- This option reduces the number of code suggestions received
-- The suggestions will focus more on identifying and fixing code problems, rather than style considerations like best practices, maintainability, or readability.
-- The suggestions will be categorized into just two groups: "Possible Issues" and "General".
+`/help_docs` is now being used to provide immediate automatic feedback to any user who [opens an issue](https://github.com/qodo-ai/pr-agent/issues/1608#issue-2897328825) on PR-Agent's open-source project
 
-Still, if you prefer the previous mode, you can set `--pr_code_suggestions.focus_only_on_problems=false` in the [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/).
+### Feb 28, 2025
+A new version, v0.27, was released. See release notes [here](https://github.com/qodo-ai/pr-agent/releases/tag/v0.27).
 
-**Example results:**
-
-Original mode
-
-<kbd><img src="https://qodo.ai/images/pr_agent/code_suggestions_original_mode.png" width="512"></kbd>
-
-Focused mode
-
-<kbd><img src="https://qodo.ai/images/pr_agent/code_suggestions_focused_mode.png" width="512"></kbd>
+### Feb 27, 2025
+- Updated the default model to `o3-mini` for all tools. You can still use the `gpt-4o` as the default model by setting the `model` parameter in the configuration file.
+- Important updates and bug fixes for Azure DevOps, see [here](https://github.com/qodo-ai/pr-agent/pull/1583)
+- Added support for adjusting the [response language](https://qodo-merge-docs.qodo.ai/usage-guide/additional_configurations/#language-settings) of the PR-Agent tools.
 
 
-### November 4, 2024
+### December 30, 2024
 
-Qodo Merge PR Agent will now leverage context from Jira or GitHub tickets to enhance the PR Feedback. Read more about this feature
-[here](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
+Following feedback from the community, we have addressed two vulnerabilities identified in the open-source PR-Agent project. The [fixes](https://github.com/qodo-ai/pr-agent/pull/1425) are now included in the newly released version (v0.26), available as of today.
 
 
 ## Overview
@@ -82,71 +87,78 @@ Qodo Merge PR Agent will now leverage context from Jira or GitHub tickets to enh
 
 Supported commands per platform:
 
-|       |                                                                                                         | GitHub             | GitLab             | Bitbucket          | Azure DevOps |
-|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:------------:|
-| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                                                                                | ✅ | ✅ | ✅ |      ✅       |
-|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Ask on code lines](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | ✅ | ✅ |                    |              |
-|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎  | ✅ |  |                    |   |
-|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎  | ✅ | ✅ |                    |   |
-|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
-|       | [PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
-|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    |              |
-|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    |              |
-|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |              |
-|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
-|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
-|       |                                                                                                         |                    |                    |                    |              |
-| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)                                                                                           | ✅ | ✅ | ✅ |      ✅       |
-|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                                                                             | ✅ |                    |                    |              |
-|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                                                                                                 | ✅ |✅| ✅ |✅|
-|       |                                                                                                         |                    |                    |                    |              |
-| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ |      ✅       |
-|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Self reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/) 💎         | ✅ | ✅ | ✅ |              |
-|       | [Global and wiki configurations](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
-|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |        ✅           |                    |              |
-|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎  | ✅ | ✅ |                    |   |
-- 💎 means this feature is available only in [PR-Agent Pro](https://www.codium.ai/pricing/)
+|       |                                                                                                         | GitHub             | GitLab             | Bitbucket | Azure DevOps |
+|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:---------:|:------------:|
+| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                 | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                               | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                       | ✅ | ✅ |     ✅     |      ✅       |
+|       | ⮑ [Ask on code lines](https://qodo-merge-docs.qodo.ai/tools/ask/#ask-lines)                             | ✅ | ✅ |           |              |
+|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Help Docs](https://qodo-merge-docs.qodo.ai/tools/help_docs/?h=auto#auto-approval)                      |   ✅    |   ✅    |   ✅        |            |
+|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎            | ✅ | ✅ |     ✅     |   |
+|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎            | ✅ | ✅ |     ✅     |   |
+|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎                        | ✅ |  |           |   |
+|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎            | ✅ | ✅ |           |   |
+|       | [CI Feedback](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |           |              |
+|       | [PR Documentation](https://qodo-merge-docs.qodo.ai/tools/documentation/) 💎                             | ✅ | ✅ |           |              |
+|       | [Custom Labels](https://qodo-merge-docs.qodo.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |           |              |
+|       | [Analyze](https://qodo-merge-docs.qodo.ai/tools/analyze/) 💎                                            | ✅ | ✅ |           |              |
+|       | [Similar Code](https://qodo-merge-docs.qodo.ai/tools/similar_code/) 💎                                  | ✅ |                    |           |              |
+|       | [Custom Prompt](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ |     ✅     |              |
+|       | [Test](https://qodo-merge-docs.qodo.ai/tools/test/) 💎                                                  | ✅ | ✅ |           |              |
+|       | [Implement](https://qodo-merge-docs.qodo.ai/tools/implement/) 💎                                        | ✅ | ✅ |     ✅     |              |
+|       | [Auto-Approve](https://qodo-merge-docs.qodo.ai/tools/improve/?h=auto#auto-approval) 💎                  |   ✅    |   ✅    |   ✅        |            |
+|       |                                                                                                         |                    |                    |           |              |
+| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                | ✅ | ✅ |     ✅     |      ✅       |
+|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)          | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                         | ✅ |                    |           |              |
+|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                  | ✅ |✅|     ✅     |✅|
+|       |                                                                                                         |                    |                    |           |              |
+| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                  | ✅ | ✅ |     ✅     |      ✅       |
+|       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)                   | ✅ | ✅ |     ✅     | ✅             |
+|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)                      | ✅ | ✅ |     ✅     | ✅             |
+|       | [Self reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)                      | ✅ | ✅ |     ✅     | ✅             |
+|       | [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/) 💎         | ✅ | ✅ |           |              |
+|       | [Global and wiki configurations](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ |     ✅     |              |
+|       | [PR interactive actions](https://www.qodo.ai/images/pr_agent/pr-actions.mp4) 💎                         | ✅ |        ✅           |           |              |
+|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎               | ✅ | ✅ |           |   |
+- 💎 means this feature is available only in [Qodo-Merge](https://www.qodo.ai/pricing/)
 
 [//]: # (- Support for additional git providers is described in [here]&#40;./docs/Full_environments.md&#41;)
 ___
 
-‣ **Auto Description ([`/describe`](https://pr-agent-docs.codium.ai/tools/describe/))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
+‣ **Auto Description ([`/describe`](https://qodo-merge-docs.qodo.ai/tools/describe/))**: Automatically generating PR description - title, type, summary, code walkthrough and labels.
 \
-‣ **Auto Review ([`/review`](https://pr-agent-docs.codium.ai/tools/review/))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
+‣ **Auto Review ([`/review`](https://qodo-merge-docs.qodo.ai/tools/review/))**: Adjustable feedback about the PR, possible issues, security concerns, review effort and more.
 \
-‣ **Code Suggestions ([`/improve`](https://pr-agent-docs.codium.ai/tools/improve/))**: Code suggestions for improving the PR.
+‣ **Code Suggestions ([`/improve`](https://qodo-merge-docs.qodo.ai/tools/improve/))**: Code suggestions for improving the PR.
 \
-‣ **Question Answering ([`/ask ...`](https://pr-agent-docs.codium.ai/tools/ask/))**: Answering free-text questions about the PR.
+‣ **Question Answering ([`/ask ...`](https://qodo-merge-docs.qodo.ai/tools/ask/))**: Answering free-text questions about the PR.
 \
-‣ **Update Changelog ([`/update_changelog`](https://pr-agent-docs.codium.ai/tools/update_changelog/))**: Automatically updating the CHANGELOG.md file with the PR changes.
+‣ **Update Changelog ([`/update_changelog`](https://qodo-merge-docs.qodo.ai/tools/update_changelog/))**: Automatically updating the CHANGELOG.md file with the PR changes.
 \
-‣ **Find Similar Issue ([`/similar_issue`](https://pr-agent-docs.codium.ai/tools/similar_issues/))**: Automatically retrieves and presents similar issues.
+‣ **Help Docs ([`/help_docs`](https://qodo-merge-docs.qodo.ai/tools/help_docs/))**: Answers a question on any repository by utilizing given documentation.
 \
-‣ **Add Documentation 💎  ([`/add_docs`](https://pr-agent-docs.codium.ai/tools/documentation/))**: Generates documentation to methods/functions/classes that changed in the PR.
+‣ **Add Documentation 💎  ([`/add_docs`](https://qodo-merge-docs.qodo.ai/tools/documentation/))**: Generates documentation to methods/functions/classes that changed in the PR.
 \
-‣ **Generate Custom Labels 💎 ([`/generate_labels`](https://pr-agent-docs.codium.ai/tools/custom_labels/))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
+‣ **Generate Custom Labels 💎 ([`/generate_labels`](https://qodo-merge-docs.qodo.ai/tools/custom_labels/))**: Generates custom labels for the PR, based on specific guidelines defined by the user.
 \
-‣ **Analyze 💎 ([`/analyze`](https://pr-agent-docs.codium.ai/tools/analyze/))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
+‣ **Analyze 💎 ([`/analyze`](https://qodo-merge-docs.qodo.ai/tools/analyze/))**: Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component.
 \
-‣ **Custom Prompt 💎 ([`/custom_prompt`](https://pr-agent-docs.codium.ai/tools/custom_prompt/))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
+‣ **Test 💎 ([`/test`](https://qodo-merge-docs.qodo.ai/tools/test/))**: Generate tests for a selected component, based on the PR code changes.
 \
-‣ **Generate Tests 💎 ([`/test component_name`](https://pr-agent-docs.codium.ai/tools/test/))**: Generates unit tests for a selected component, based on the PR code changes.
+‣ **Custom Prompt 💎 ([`/custom_prompt`](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/))**: Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user.
 \
-‣ **CI Feedback 💎 ([`/checks ci_job`](https://pr-agent-docs.codium.ai/tools/ci_feedback/))**: Automatically generates feedback and analysis for a failed CI job.
+‣ **Generate Tests 💎 ([`/test component_name`](https://qodo-merge-docs.qodo.ai/tools/test/))**: Generates unit tests for a selected component, based on the PR code changes.
 \
-‣ **Similar Code 💎 ([`/find_similar_component`](https://pr-agent-docs.codium.ai/tools/similar_code/))**: Retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+‣ **CI Feedback 💎 ([`/checks ci_job`](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/))**: Automatically generates feedback and analysis for a failed CI job.
+\
+‣ **Similar Code 💎 ([`/find_similar_component`](https://qodo-merge-docs.qodo.ai/tools/similar_code/))**: Retrieves the most similar code components from inside the organization's codebase, or from open-source code.
+\
+‣ **Implement 💎 ([`/implement`](https://qodo-merge-docs.qodo.ai/tools/implement/))**: Generates implementation code from review suggestions.
 ___
 
 ## Example results
@@ -179,43 +191,6 @@ ___
 </div>
 
 
-
-
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/78#issuecomment-1639739496">/reflect_and_review:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/reflect_and_review.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
-
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695020538">/ask:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/ask-2.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
-
-[//]: # (<h4><a href="https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695024952">/improve:</a></h4>)
-
-[//]: # (<div align="center">)
-
-[//]: # (<p float="center">)
-
-[//]: # (<img src="https://www.codium.ai/images/improve-2.gif" width="800">)
-
-[//]: # (</p>)
-
-[//]: # (</div>)
 <div align="left">
 
 
@@ -225,7 +200,7 @@ ___
 
 ## Try it now
 
-Try the GPT-4 powered PR-Agent instantly on _your public GitHub repository_. Just mention `@CodiumAI-Agent` and add the desired command in any PR comment. The agent will generate a response based on your command.
+Try the Claude Sonnet powered PR-Agent instantly on _your public GitHub repository_. Just mention `@CodiumAI-Agent` and add the desired command in any PR comment. The agent will generate a response based on your command.
 For example, add a comment to any pull request with the following text:
 ```
 @CodiumAI-Agent /review
@@ -236,22 +211,16 @@ Note that this is a promotional bot, suitable only for initial experimentation.
 It does not have 'edit' access to your repo, for example, so it cannot update the PR description or add labels (`@CodiumAI-Agent /describe` will publish PR description as a comment). In addition, the bot cannot be used on private repositories, as it does not have access to the files there.
 
 
-![Review generation process](https://www.codium.ai/images/demo-2.gif)
-
-
-To set up your own PR-Agent, see the [Installation](https://pr-agent-docs.codium.ai/installation/) section below.
-Note that when you set your own PR-Agent or use CodiumAI hosted PR-Agent, there is no need to mention `@CodiumAI-Agent ...`. Instead, directly start with the command, e.g., `/ask ...`.
-
 ---
 
 
-## PR-Agent Pro 💎
-[PR-Agent Pro](https://www.codium.ai/pricing/) is a hosted version of PR-Agent, provided by CodiumAI. It is available for a monthly fee, and provides the following benefits:
-1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the PR-Agent app to your GitHub\GitLab\BitBucket repo.
-2. **Improved privacy** - No data will be stored or used to train models. PR-Agent Pro will employ zero data retention, and will use an OpenAI account with zero data retention.
-3. **Improved support** - PR-Agent Pro users will receive priority support, and will be able to request new features and capabilities.
-4. **Extra features** -In addition to the benefits listed above, PR-Agent Pro will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results.
-See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of features available in PR-Agent Pro.
+## Qodo Merge 💎
+[Qodo Merge](https://www.qodo.ai/pricing/) is a hosted version of PR-Agent, provided by Qodo. It is available for a monthly fee, and provides the following benefits:
+1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the Qodo Merge app to your GitHub\GitLab\BitBucket repo.
+2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge will employ zero data retention, and will use an OpenAI account with zero data retention.
+3. **Improved support** - Qodo Merge users will receive priority support, and will be able to request new features and capabilities.
+4. **Extra features** -In addition to the benefits listed above, Qodo Merge will emphasize more customization, and the usage of static code analysis, in addition to LLM logic, to improve results.
+See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of features available in Qodo Merge.
 
 
 
@@ -259,9 +228,9 @@ See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for a list of
 
 The following diagram illustrates PR-Agent tools and their flow:
 
-![PR-Agent Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
+![PR-Agent Tools](https://www.qodo.ai/images/pr_agent/diagram-v0.9.png)
 
-Check out the [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy) page for more details on how we convert a code diff to a manageable LLM prompt
+Check out the [PR Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/#pr-compression-strategy) page for more details on how we convert a code diff to a manageable LLM prompt
 
 ## Why use PR-Agent?
 
@@ -269,10 +238,10 @@ A reasonable question that can be asked is: `"Why use PR-Agent? What makes it st
 
 Here are some advantages of PR-Agent:
 
-- We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single GPT-4 call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
-- Our [PR Compression strategy](https://pr-agent-docs.codium.ai/core-abilities/#pr-compression-strategy)  is a core ability that enables to effectively tackle both short and long PRs.
+- We emphasize **real-life practical usage**. Each tool (review, improve, ask, ...) has a single LLM call, no more. We feel that this is critical for realistic team usage - obtaining an answer quickly (~30 seconds) and affordably.
+- Our [PR Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/#pr-compression-strategy)  is a core ability that enables to effectively tackle both short and long PRs.
 - Our JSON prompting strategy enables to have **modular, customizable tools**. For example, the '/review' tool categories can be controlled via the [configuration](pr_agent/settings/configuration.toml) file. Adding additional categories is easy and accessible.
-- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT-4, GPT-3.5, Anthropic, Cohere, Llama2).
+- We support **multiple git providers** (GitHub, Gitlab, Bitbucket), **multiple ways** to use the tool (CLI, GitHub Action, GitHub App, Docker, ...), and **multiple models** (GPT, Claude, Deepseek, ...)
 
 
 ## Data privacy
@@ -282,24 +251,22 @@ Here are some advantages of PR-Agent:
 - If you host PR-Agent with your OpenAI API key, it is between you and OpenAI. You can read their API data privacy policy here:
 https://openai.com/enterprise-privacy
 
-### CodiumAI-hosted PR-Agent Pro 💎
+### Qodo-hosted Qodo Merge 💎
 
-- When using PR-Agent Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+- When using Qodo Merge 💎, hosted by Qodo, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
 
-- For certain clients, CodiumAI-hosted PR-Agent Pro will use CodiumAI’s proprietary models — if this is the case, you will be notified.
+- For certain clients, Qodo-hosted Qodo Merge will use Qodo’s proprietary models — if this is the case, you will be notified.
 
-- No passive collection of Code and Pull Requests’ data — PR-Agent will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
+- No passive collection of Code and Pull Requests’ data — Qodo Merge will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
 
-### PR-Agent Chrome extension
+### Qodo Merge Chrome extension
 
-- The [PR-Agent Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of PR-Agent.
+- The [Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/qodo-merge-ai-powered-cod/ephlnjeghhogofkifjloamocljapahnl) serves solely to modify the visual appearance of a GitHub PR screen. It does not transmit any user's repo or pull request code. Code is only sent for processing when a user submits a GitHub comment that activates a PR-Agent tool, in accordance with the standard privacy policy of Qodo-Merge.
 
 ## Links
 
-[![Join our Discord community](https://raw.githubusercontent.com/Codium-ai/codiumai-vscode-release/main/media/docs/Joincommunity.png)](https://discord.gg/kG35uSHDBc)
-
 - Discord community: https://discord.gg/kG35uSHDBc
-- CodiumAI site: https://codium.ai
-- Blog: https://www.codium.ai/blog/
-- Troubleshooting: https://www.codium.ai/blog/technical-faq-and-troubleshooting/
-- Support: support@codium.ai
+- Qodo site: https://www.qodo.ai/
+- Blog: https://www.qodo.ai/blog/
+- Troubleshooting: https://www.qodo.ai/blog/technical-faq-and-troubleshooting/
+- Support: support@qodo.ai

SECURITY.md

@@ -0,0 +1,62 @@
+# Security Policy
+
+PR-Agent is an open-source tool to help efficiently review and handle pull requests. Qodo Merge is a paid version of PR-Agent, designed for companies and teams that require additional features and capabilities. 
+
+This document describes the security policy of PR-Agent. For Qodo Merge's security policy, see [here](https://qodo-merge-docs.qodo.ai/overview/data_privacy/#qodo-merge).
+
+## PR-Agent Self-Hosted Solutions
+
+When using PR-Agent with your OpenAI (or other LLM provider) API key, the security relationship is directly between you and the provider. We do not send your code to Qodo servers.
+
+Types of [self-hosted solutions](https://qodo-merge-docs.qodo.ai/installation):
+- Locally
+- GitHub integration
+- GitLab integration
+- BitBucket integration
+- Azure DevOps integration
+
+
+## PR-Agent Supported Versions
+
+This section outlines which versions of PR-Agent are currently supported with security updates.
+
+### Docker Deployment Options
+
+#### Latest Version
+
+For the most recent updates, use our latest Docker image which is automatically built nightly:
+```yaml
+uses: qodo-ai/pr-agent@main
+```
+
+#### Specific Release Version
+
+For a fixed version, you can pin your action to a specific release version. Browse available releases at:
+[PR-Agent Releases](https://github.com/qodo-ai/pr-agent/releases)
+
+For example, to github action:
+
+```yaml
+steps:
+  - name: PR Agent action step
+    id: pragent
+    uses: docker://codiumai/pr-agent:0.26-github_action
+```
+
+#### Enhanced Security with Docker Digest
+
+For maximum security, you can specify the Docker image using its digest:
+```yaml
+steps:
+  - name: PR Agent action step
+    id: pragent
+    uses: docker://codiumai/pr-agent@sha256:14165e525678ace7d9b51cda8652c2d74abb4e1d76b57c4a6ccaeba84663cc64
+```
+
+## Reporting a Vulnerability
+
+We take the security of PR-Agent seriously. If you discover a security vulnerability, please report it immediately to:
+
+Email: tal.r@qodo.ai
+
+Please include a description of the vulnerability, steps to reproduce, and the affected PR-Agent version.

best_practices.md

@@ -0,0 +1,199 @@
+
+<b>Pattern 1: Wrap critical operations with try-except blocks to handle potential exceptions, especially for file operations, API calls, and data parsing functions.</b>
+
+Example code before:
+```
+def get_git_repo_url(self, issues_or_pr_url: str) -> str:
+    repo_path = self._get_owner_and_repo_path(issues_or_pr_url)
+    if not repo_path or repo_path not in issues_or_pr_url:
+        get_logger().error(f"Unable to retrieve owner/path from url: {issues_or_pr_url}")
+        return ""
+    return f"{issues_or_pr_url.split(repo_path)[0]}{repo_path}.git"
+```
+
+Example code after:
+```
+def get_git_repo_url(self, issues_or_pr_url: str) -> str:
+    try:
+        repo_path = self._get_owner_and_repo_path(issues_or_pr_url)
+        if not repo_path or repo_path not in issues_or_pr_url:
+            get_logger().error(f"Unable to retrieve owner/path from url: {issues_or_pr_url}")
+            return ""
+        return f"{issues_or_pr_url.split(repo_path)[0]}{repo_path}.git"
+    except Exception as e:
+        get_logger().error(f"Failed to get git repo url from {issues_or_pr_url}, error: {e}")
+        return ""
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1644#discussion_r2013912636
+- https://github.com/qodo-ai/pr-agent/pull/1263#discussion_r1782129216
+- https://github.com/qodo-ai/pr-agent/pull/1391#discussion_r1879870807
+</details>
+
+
+___
+
+<b>Pattern 2: Use proper logging methods instead of print statements, with get_logger().error() for errors, get_logger().warning() for warnings, and get_logger().info() for informational messages.</b>
+
+Example code before:
+```
+if isinstance(response_tuple, tuple) and len(response_tuple) == 3:
+    response_json = json.loads(response_tuple[2])
+else:
+    print("Unexpected response format:", response_tuple)
+    return sub_issues
+```
+
+Example code after:
+```
+if isinstance(response_tuple, tuple) and len(response_tuple) == 3:
+    response_json = json.loads(response_tuple[2])
+else:
+    get_logger().error(f"Unexpected response format", artifact={"response": response_tuple})
+    return sub_issues
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1958684550
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1958686068
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1964110734
+- https://github.com/qodo-ai/pr-agent/pull/1634#discussion_r2007976915
+</details>
+
+
+___
+
+<b>Pattern 3: Move specific imports to where they are actually used rather than at the top of the file, especially for rarely used or heavy dependencies.</b>
+
+Example code before:
+```
+import os
+from azure.identity import ClientSecretCredential
+import litellm
+import openai
+import requests
+```
+
+Example code after:
+```
+import os
+import litellm
+import openai
+import requests
+
+# Later in the code where Azure AD is actually used:
+if get_settings().get("AZURE_AD.CLIENT_ID", None):
+    from azure.identity import ClientSecretCredential
+    # Azure AD specific code...
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1698#discussion_r2046221654
+</details>
+
+
+___
+
+<b>Pattern 4: Add defensive checks for potentially None or invalid values before performing operations on them, especially when working with external data or API responses.</b>
+
+Example code before:
+```
+model_is_from_o_series = re.match(r"^o[1-9](-mini|-preview)?$", model)
+if ('gpt' in get_settings().config.model.lower() or model_is_from_o_series) and get_settings().get('openai.key'):
+    return encoder_estimate
+```
+
+Example code after:
+```
+if model is None:
+    get_logger().warning("Model is None, cannot determine model type accurately")
+    return encoder_estimate
+
+if not isinstance(model, str):
+    get_logger().warning(f"Model is not a string type: {type(model)}")
+    return encoder_estimate
+    
+model_is_from_o_series = re.match(r"^o[1-9](-mini|-preview)?$", model)
+openai_key_exists = get_settings().get('openai.key') is not None
+
+if (('gpt' in model.lower() or model_is_from_o_series) and openai_key_exists):
+    return encoder_estimate
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1644#discussion_r2032621065
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1958694146
+- https://github.com/qodo-ai/pr-agent/pull/1391#discussion_r1879875496
+</details>
+
+
+___
+
+<b>Pattern 5: Avoid redundant code initialization and reuse existing objects or instances when possible, especially for resource-intensive operations.</b>
+
+Example code before:
+```
+if tickets:
+    provider = GithubProvider()
+    
+    for ticket in tickets:
+        # Extract sub-issues
+        sub_issues_content = []
+        try:
+            sub_issues = provider.fetch_sub_issues(ticket)
+```
+
+Example code after:
+```
+if tickets:
+    for ticket in tickets:
+        # Extract sub-issues
+        sub_issues_content = []
+        try:
+            sub_issues = git_provider.fetch_sub_issues(ticket)
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1964085987
+- https://github.com/qodo-ai/pr-agent/pull/1529#discussion_r1964088304
+</details>
+
+
+___
+
+<b>Pattern 6: Use descriptive variable names and add explanatory comments for complex logic or non-obvious code to improve maintainability and readability.</b>
+
+Example code before:
+```
+issues = value
+for i, issue in enumerate(issues):
+    try:
+        if not issue or not isinstance(issue, dict):
+            continue
+```
+
+Example code after:
+```
+focus_areas = value
+for i, focus_area in enumerate(focus_areas):
+    try:
+        # Skip empty issues or non-dictionary items to ensure valid data structure
+        if not focus_area or not isinstance(focus_area, dict):
+            continue
+```
+
+<details><summary>Examples for relevant past discussions:</summary>
+
+- https://github.com/qodo-ai/pr-agent/pull/1262#discussion_r1782097201
+- https://github.com/qodo-ai/pr-agent/pull/1262#discussion_r1782097204
+- https://github.com/qodo-ai/pr-agent/pull/1583#discussion_r1971790979
+</details>
+
+
+___

docker/Dockerfile

@@ -4,7 +4,7 @@ WORKDIR /app
 ADD pyproject.toml .
 ADD requirements.txt .
 ADD docs docs
-RUN pip install . && rm pyproject.toml requirements.txt
+RUN pip install --no-cache-dir . && rm pyproject.toml requirements.txt
 ENV PYTHONPATH=/app
 
 FROM base AS github_app
@@ -33,7 +33,7 @@ CMD ["python", "pr_agent/servers/azuredevops_server_webhook.py"]
 
 FROM base AS test
 ADD requirements-dev.txt .
-RUN pip install -r requirements-dev.txt && rm requirements-dev.txt
+RUN pip install --no-cache-dir -r requirements-dev.txt && rm requirements-dev.txt
 ADD pr_agent pr_agent
 ADD tests tests
 

docker/Dockerfile.lambda

@@ -1,12 +1,12 @@
-FROM public.ecr.aws/lambda/python:3.10
+FROM public.ecr.aws/lambda/python:3.12
 
-RUN yum update -y && \
-    yum install -y gcc python3-devel git && \
-    yum clean all
+RUN dnf update -y && \
+    dnf install -y gcc python3-devel git && \
+    dnf clean all
 
-ADD pyproject.toml requirements.txt .
-RUN pip install . && rm pyproject.toml
-RUN pip install mangum==0.17.0
+ADD pyproject.toml requirements.txt ./
+RUN pip install --no-cache-dir . && rm pyproject.toml
+RUN pip install --no-cache-dir mangum==0.17.0
 COPY pr_agent/ ${LAMBDA_TASK_ROOT}/pr_agent/
 
 CMD ["pr_agent.servers.serverless.serverless"]

docs/docs/ai_search/index.md

@@ -0,0 +1,315 @@
+<div class="search-section">
+    <h1>AI Docs Search</h1>
+    <p class="search-description">
+        Search through our documentation using AI-powered natural language queries.
+    </p>
+    <div class="search-container">
+        <input 
+            type="text" 
+            id="searchInput" 
+            class="search-input" 
+            placeholder="Enter your search term..."
+        >
+        <button id="searchButton" class="search-button">Search</button>
+    </div>
+    <div id="spinner" class="spinner-container" style="display: none;">
+        <div class="spinner"></div>
+    </div>
+    <div id="results" class="results-container"></div>
+</div>
+
+<style>
+Untitled
+.search-section {
+    max-width: 800px;
+    margin: 0 auto;
+    padding: 0 1rem 2rem;
+}
+
+h1 {
+    color: #666;
+    font-size: 2.125rem;
+    font-weight: normal;
+    margin-bottom: 1rem;
+}
+
+.search-description {
+    color: #666;
+    font-size: 1rem;
+    line-height: 1.5;
+    margin-bottom: 2rem;
+    max-width: 800px;
+}
+
+.search-container {
+    display: flex;
+    gap: 1rem;
+    max-width: 800px;
+    margin: 0;  /* Changed from auto to 0 to align left */
+}
+
+.search-input {
+    flex: 1;
+    padding: 0 0.875rem;
+    border: 1px solid #ddd;
+    border-radius: 4px;
+    font-size: 0.9375rem;
+    outline: none;
+    height: 40px;  /* Explicit height */
+}
+
+.search-input:focus {
+    border-color: #6c63ff;
+}
+
+.search-button {
+    padding: 0 1.25rem;
+    background-color: #2196F3;
+    color: white;
+    border: none;
+    border-radius: 4px;
+    cursor: pointer;
+    font-size: 0.875rem;
+    transition: background-color 0.2s;
+    height: 40px;  /* Match the height of search input */
+    display: flex;
+    align-items: center;
+    justify-content: center;
+}
+
+.search-button:hover {
+    background-color: #1976D2;
+}
+
+.spinner-container {
+    display: flex;
+    justify-content: center;
+    margin-top: 2rem;
+}
+
+.spinner {
+    width: 40px;
+    height: 40px;
+    border: 4px solid #f3f3f3;
+    border-top: 4px solid #2196F3;
+    border-radius: 50%;
+    animation: spin 1s linear infinite;
+}
+
+@keyframes spin {
+    0% { transform: rotate(0deg); }
+    100% { transform: rotate(360deg); }
+}
+
+.results-container {
+    margin-top: 2rem;
+    max-width: 800px;
+}
+
+.result-item {
+    padding: 1rem;
+    border: 1px solid #ddd;
+    border-radius: 4px;
+    margin-bottom: 1rem;
+}
+
+.result-title {
+    font-size: 1.2rem;
+    color: #2196F3;
+    margin-bottom: 0.5rem;
+}
+
+.result-description {
+    color: #666;
+}
+
+.error-message {
+    color: #dc3545;
+    padding: 1rem;
+    border: 1px solid #dc3545;
+    border-radius: 4px;
+    margin-top: 1rem;
+}
+
+.markdown-content {
+    line-height: 1.6;
+    color: var(--md-typeset-color);
+    background: var(--md-default-bg-color);
+    border: 1px solid var(--md-default-fg-color--lightest);
+    border-radius: 12px;
+    padding: 1.5rem;
+    box-shadow: 0 2px 4px rgba(0,0,0,0.05);
+    position: relative;
+    margin-top: 2rem;
+}
+
+.markdown-content::before {
+    content: '';
+    position: absolute;
+    top: -8px;
+    left: 24px;
+    width: 16px;
+    height: 16px;
+    background: var(--md-default-bg-color);
+    border-left: 1px solid var(--md-default-fg-color--lightest);
+    border-top: 1px solid var(--md-default-fg-color--lightest);
+    transform: rotate(45deg);
+}
+
+.markdown-content > *:first-child {
+    margin-top: 0;
+    padding-top: 0;
+}
+
+.markdown-content p {
+    margin-bottom: 1rem;
+}
+
+.markdown-content p:last-child {
+    margin-bottom: 0;
+}
+
+.markdown-content code {
+    background: var(--md-code-bg-color);
+    color: var(--md-code-fg-color);
+    padding: 0.2em 0.4em;
+    border-radius: 3px;
+    font-size: 0.9em;
+    font-family: ui-monospace, SFMono-Regular, SF Mono, Menlo, Consolas, Liberation Mono, monospace;
+}
+
+.markdown-content pre {
+    background: var(--md-code-bg-color);
+    padding: 1rem;
+    border-radius: 6px;
+    overflow-x: auto;
+    margin: 1rem 0;
+}
+
+.markdown-content pre code {
+    background: none;
+    padding: 0;
+    font-size: 0.9em;
+}
+
+[data-md-color-scheme="slate"] .markdown-content {
+    box-shadow: 0 2px 4px rgba(0,0,0,0.1);
+}
+
+</style>
+
+<script src="https://cdnjs.cloudflare.com/ajax/libs/marked/9.1.6/marked.min.js"></script>
+
+<script>
+window.addEventListener('load', function() {
+    function displayResults(responseText) {
+        const resultsContainer = document.getElementById('results');
+        const spinner = document.getElementById('spinner');
+        const searchContainer = document.querySelector('.search-container');
+        
+        // Hide spinner
+        spinner.style.display = 'none';
+        
+        // Scroll to search bar
+        searchContainer.scrollIntoView({ behavior: 'smooth', block: 'start' });
+        
+        try {
+            const results = JSON.parse(responseText);
+
+            marked.setOptions({
+                breaks: true,
+                gfm: true,
+                headerIds: false,
+                sanitize: false
+            });
+
+            const htmlContent = marked.parse(results.message);
+            
+            resultsContainer.className = 'markdown-content';
+            resultsContainer.innerHTML = htmlContent;
+
+            // Scroll after content is rendered
+            setTimeout(() => {
+                const searchContainer = document.querySelector('.search-container');
+                const offset = 55; // Offset from top in pixels
+                const elementPosition = searchContainer.getBoundingClientRect().top;
+                const offsetPosition = elementPosition + window.pageYOffset - offset;
+                
+                window.scrollTo({
+                    top: offsetPosition,
+                    behavior: 'smooth'
+                });
+            }, 100);
+        } catch (error) {
+            console.error('Error parsing results:', error);
+            resultsContainer.innerHTML = '<div class="error-message">Error processing results</div>';
+        }
+    }
+
+    async function performSearch() {
+        const searchInput = document.getElementById('searchInput');
+        const resultsContainer = document.getElementById('results');
+        const spinner = document.getElementById('spinner');
+        const searchTerm = searchInput.value.trim();
+
+        if (!searchTerm) {
+            resultsContainer.innerHTML = '<div class="error-message">Please enter a search term</div>';
+            return;
+        }
+
+        // Show spinner, clear results
+        spinner.style.display = 'flex';
+        resultsContainer.innerHTML = '';
+
+        try { 
+            const data = {
+                "query": searchTerm
+            };
+
+            const options = {
+                method: 'POST',
+                headers: {
+                    'accept': 'text/plain',
+                    'content-type': 'application/json',
+                },
+                body: JSON.stringify(data)
+            };
+
+            // const API_ENDPOINT = 'http://0.0.0.0:3000/api/v1/docs_help';
+            const API_ENDPOINT = 'https://help.merge.qodo.ai/api/v1/docs_help';
+
+            const response = await fetch(API_ENDPOINT, options);
+
+            if (!response.ok) {
+                throw new Error(`HTTP error! status: ${response.status}`);
+            }
+
+            const responseText = await response.text();
+            displayResults(responseText);
+        } catch (error) {
+            spinner.style.display = 'none';
+            resultsContainer.innerHTML = `
+                <div class="error-message">
+                    An error occurred while searching. Please try again later.
+                </div>
+            `;
+        }
+    }
+
+    // Add event listeners
+    const searchButton = document.getElementById('searchButton');
+    const searchInput = document.getElementById('searchInput');
+    
+    if (searchButton) {
+        searchButton.addEventListener('click', performSearch);
+    }
+    
+    if (searchInput) {
+        searchInput.addEventListener('keypress', function(e) {
+            if (e.key === 'Enter') {
+                performSearch();
+            }
+        });
+    }
+});
+</script>

docs/docs/chrome-extension/data_privacy.md

@@ -1,4 +1,4 @@
 We take your code's security and privacy seriously:
 
 - The Chrome extension will not send your code to any external servers.
-- For private repositories, we will first validate the user's identity and permissions. After authentication, we generate responses using the existing Qodo Merge Pro integration.
+- For private repositories, we will first validate the user's identity and permissions. After authentication, we generate responses using the existing Qodo Merge integration.

docs/docs/chrome-extension/features.md

@@ -8,7 +8,7 @@ To enable private chat, simply install the Qodo Merge Chrome extension. After in
 This chat session is **private**, and won't be visible to other users.
 
 All open-source repositories are supported.
-For private repositories, you will also need to install Qodo Merge Pro, After installation, make sure to open at least one new PR to fully register your organization. Once done, you can chat with both new and existing PRs across all installed repositories.
+For private repositories, you will also need to install Qodo Merge. After installation, make sure to open at least one new PR to fully register your organization. Once done, you can chat with both new and existing PRs across all installed repositories.
 
 #### Context-aware PR chat
 

docs/docs/chrome-extension/index.md

@@ -1,11 +1,11 @@
-[Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl) is a collection of tools that integrates seamlessly with your GitHub environment, aiming to enhance your Git usage experience, and providing AI-powered capabilities to your PRs.
+[Qodo Merge Chrome extension](https://chromewebstore.google.com/detail/pr-agent-chrome-extension/ephlnjeghhogofkifjloamocljapahnl){:target="_blank"} is a collection of tools that integrates seamlessly with your GitHub environment, aiming to enhance your Git usage experience, and providing AI-powered capabilities to your PRs.
 
 With a single-click installation you will gain access to a context-aware chat on your pull requests code, a toolbar extension with multiple AI feedbacks, Qodo Merge filters, and additional abilities.
 
-The extension is powered by top code models like Claude 3.5 Sonnet and GPT4. All the extension's features are free to use on public repositories.
+The extension is powered by top code models like Claude 3.7 Sonnet and o3-mini. All the extension's features are free to use on public repositories.
 
-For private repositories, you will need to install [Qodo Merge Pro](https://github.com/apps/qodo-merge-pro) in addition to the extension  (Quick GitHub app setup with a 14-day free trial. No credit card needed).
-For a demonstration of how to install Qodo Merge Pro and use it with the Chrome extension, please refer to the tutorial video at the provided [link](https://codium.ai/images/pr_agent/private_repos.mp4).
+For private repositories, you will need to install [Qodo Merge](https://github.com/apps/qodo-merge-pro){:target="_blank"} in addition to the extension  (Quick GitHub app setup with a 14-day free trial. No credit card needed).
+For a demonstration of how to install Qodo Merge and use it with the Chrome extension, please refer to the tutorial video at the provided [link](https://codium.ai/images/pr_agent/private_repos.mp4){:target="_blank"}.
 
 <img src="https://codium.ai/images/pr_agent/PR-AgentChat.gif" width="768">
 

docs/docs/chrome-extension/options.md

@@ -0,0 +1,41 @@
+## Options and Configurations
+
+### Accessing the Options Page
+
+To access the options page for the Qodo Merge Chrome extension:
+
+1. Find the extension icon in your Chrome toolbar (usually in the top-right corner of your browser)
+2. Right-click on the extension icon
+3. Select "Options" from the context menu that appears
+
+Alternatively, you can access the options page directly using this URL:
+
+[chrome-extension://ephlnjeghhogofkifjloamocljapahnl/options.html](chrome-extension://ephlnjeghhogofkifjloamocljapahnl/options.html)
+
+<img src="https://codium.ai/images/pr_agent/chrome_ext_options.png" width="256">
+
+
+### Configuration Options
+
+<img src="https://codium.ai/images/pr_agent/chrome_ext_settings_page.png" width="512">
+
+
+#### API Base Host
+
+For single-tenant customers, you can configure the extension to communicate directly with your company's Qodo Merge server instance.
+
+To set this up:
+
+- Enter your organization's Qodo Merge API endpoint in the "API Base Host" field
+- This endpoint should be provided by your Qodo DevOps Team
+
+*Note: The extension does not send your code to the server, but only triggers your previously installed Qodo Merge application.*
+
+#### Interface Options
+
+You can customize the extension's interface by:
+
+- Toggling the "Show Qodo Merge Toolbar" option
+- When disabled, the toolbar will not appear in your Github comment bar
+
+Remember to click "Save Settings" after making any changes.

docs/docs/core-abilities/auto_best_practices.md

@@ -0,0 +1,69 @@
+# Auto Best Practices 💎
+`Supported Git Platforms: GitHub`
+
+## Overview
+
+![Auto best practice suggestion graph](https://www.qodo.ai/images/pr_agent/auto_best_practices_graph.png){width=684}
+
+> Note - enabling a [Wiki](https://qodo-merge-docs.qodo.ai/usage-guide/enabling_a_wiki/) is required for this feature.
+
+### Finding Code Problems - Exploration Phase
+
+The `improve` tool identifies potential issues, problems and bugs in Pull Request (PR) code changes. 
+Rather than focusing on minor issues like code style or formatting, the tool intelligently analyzes code to detect meaningful problems. 
+
+The analysis intentionally takes a flexible, _exploratory_ approach to identify meaningful potential issues, allowing the tool to surface relevant code suggestions without being constrained by predefined categories.
+
+### Tracking Implemented Suggestions
+
+Qodo Merge features a novel [tracking system](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) that automatically detects when PR authors implement AI-generated code suggestions. 
+All accepted suggestions are aggregated in a repository-specific wiki page called [`.pr_agent_accepted_suggestions`](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_accepted_suggestions)
+
+
+### Learning and Applying Auto Best Practices
+
+Monthly, Qodo Merge analyzes the collection of accepted suggestions to generate repository-specific best practices, stored in [`.pr_agent_auto_best_practices`](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_auto_best_practices) wiki file.
+These best practices reflect recurring patterns in accepted code improvements.
+
+The `improve` tool will incorporate these best practices as an additional analysis layer, checking PR code changes against known patterns of previously accepted improvements.
+This creates a two-phase analysis:
+
+1. Open exploration for general code issues
+2. Targeted checking against established best practices - exploiting the knowledge gained from past suggestions
+
+By keeping these phases decoupled, the tool remains free to discover new or unseen issues and problems, while also learning from past experiences.
+
+
+When presenting the suggestions generated by the `improve` tool, Qodo Merge will add a dedicated label for each suggestion generated from the auto best practices - 'Learned best practice':
+
+![Auto best practice suggestion](https://www.qodo.ai/images/pr_agent/auto_best_practices.png){width=684}
+
+
+## Auto Best Practices vs Custom Best Practices
+
+Teams and companies can also manually define their own [custom best practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) in Qodo Merge. 
+
+When custom best practices exist, Qodo Merge will still generate an 'auto best practices' wiki file, though it won't be used by the `improve` tool. 
+However, this auto-generated file can still serve two valuable purposes:
+
+1. It can help enhance your custom best practices with additional insights derived from suggestions your team found valuable enough to implement
+2. It demonstrates effective patterns for writing AI-friendly best practices
+
+Even when using custom best practices, we recommend regularly reviewing the auto best practices file to refine your custom rules.
+
+## Relevant configurations
+
+```toml
+[auto_best_practices]
+# Disable all auto best practices usage or generation
+enable_auto_best_practices = true  
+
+# Disable usage of auto best practices file in the 'improve' tool
+utilize_auto_best_practices = true 
+
+# Extra instructions to the auto best practices generation prompt
+extra_instructions = ""            
+
+# Max number of patterns to be detected
+max_patterns = 5                   
+```

docs/docs/core-abilities/code_oriented_yaml.md

@@ -1,2 +0,0 @@
-## Overview
-TBD

docs/docs/core-abilities/code_validation.md

@@ -0,0 +1,39 @@
+## Introduction
+The Git environment usually represents the final stage before code enters production. Hence, Detecting bugs and issues during the review process is critical.
+
+The [`improve`](https://qodo-merge-docs.qodo.ai/tools/improve/) tool provides actionable code suggestions for your pull requests, aiming to help detect and fix bugs and problems.
+By default, suggestions appear as a comment in a table format:
+
+![code_suggestions_as_comment_closed.png](https://codium.ai/images/pr_agent/code_suggestions_as_comment_closed.png){width=512}
+
+![code_suggestions_as_comment_open.png](https://codium.ai/images/pr_agent/code_suggestions_as_comment_open.png){width=512}
+
+## Validation of Code Suggestions
+
+Each suggestion in the table can be "applied" by clicking on the `Apply this suggestion` checkbox, converting it to a committable Git code change that can be committed directly to the PR.
+This approach allows to fix issues without returning to your IDE for manual edits — significantly faster and more convenient.
+
+However, committing a suggestion in a Git environment carries more risk than in a local IDE, as you don't have the opportunity to fully run and test the code before committing.
+
+To balance convenience with safety, Qodo Merge implements a dual validation system for each generated code suggestion:
+
+1) **Localization** - Qodo Merge confirms that the suggestion's line numbers and surrounding code, as predicted by the model, actually match the repo code. This means that the model correctly identified the context and location of the code to be changed.
+
+2) **"Compilation"** - Using static code analysis, Qodo Merge verifies that after applying the suggestion, the modified file will still be valid, meaning tree-sitter syntax processing will not throw an error. This process is relevant for multiple programming languages, see [here](https://pypi.org/project/tree-sitter-languages/) for the full list of supported languages.
+
+When a suggestion fails to meet these validation criteria, it may still provide valuable feedback, but isn't suitable for direct application to the PR.
+In such cases, Qodo Merge will omit the 'apply' checkbox and instead display:
+
+`[To ensure code accuracy, apply this suggestion manually]`
+
+All suggestions that pass these validations undergo a final stage of **self-reflection**, where the AI model evaluates, scores, and re-ranks its own suggestions, eliminating any that are irrelevant or incorrect.
+Read more about this process in the [self-reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/) page.
+
+## Conclusion
+
+The validation methods described above enhance the reliability of code suggestions and help PR authors determine which suggestions are safer to apply in the Git environment.
+Of course, additional factors should be considered, such as suggestion complexity and potential code impact. 
+
+Human judgment remains essential. After clicking 'apply', Qodo Merge still presents the 'before' and 'after' code snippets for review, allowing you to assess the changes before finalizing the commit.
+
+![improve](https://codium.ai/images/pr_agent/improve.png){width=512}

docs/docs/core-abilities/fetching_ticket_context.md

@@ -1,15 +1,16 @@
 # Fetching Ticket Context for PRs
-`Supported Git Platforms : GitHub, GitLab, Bitbucket`
+`Supported Git Platforms: GitHub, GitLab, Bitbucket`
 
 ## Overview
-Qodo Merge PR Agent streamlines code review workflows by seamlessly connecting with multiple ticket management systems.
+Qodo Merge streamlines code review workflows by seamlessly connecting with multiple ticket management systems.
 This integration enriches the review process by automatically surfacing relevant ticket information and context alongside code changes.
 
-## Ticket systems supported
+**Ticket systems supported**:
+
 - GitHub
 - Jira (💎)
 
-Ticket data fetched:
+**Ticket data fetched:**
 
 1. Ticket Title
 2. Ticket Description
@@ -26,7 +27,7 @@ Ticket Recognition Requirements:
 - For Jira tickets, you should follow the instructions in [Jira Integration](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#jira-integration) in order to authenticate with Jira.
 
 ### Describe tool
-Qodo Merge PR Agent will recognize the ticket and use the ticket content (title, description, labels) to provide additional context for the code changes.
+Qodo Merge will recognize the ticket and use the ticket content (title, description, labels) to provide additional context for the code changes.
 By understanding the reasoning and intent behind modifications, the LLM can offer more insightful and relevant code analysis.
 
 ### Review tool
@@ -46,41 +47,22 @@ If you want to disable this feedback, add the following line to your configurati
 require_ticket_analysis_review=false
 ```
 
-## Providers
+## GitHub Issues Integration
 
-### Github Issues Integration
-
-Qodo Merge PR Agent will automatically recognize Github issues mentioned in the PR description and fetch the issue content.
+Qodo Merge will automatically recognize GitHub issues mentioned in the PR description and fetch the issue content.
 Examples of valid GitHub issue references:
 
 - `https://github.com/<ORG_NAME>/<REPO_NAME>/issues/<ISSUE_NUMBER>`
 - `#<ISSUE_NUMBER>`
 - `<ORG_NAME>/<REPO_NAME>#<ISSUE_NUMBER>`
 
-Since Qodo Merge PR Agent is integrated with GitHub, it doesn't require any additional configuration to fetch GitHub issues.
+Since Qodo Merge is integrated with GitHub, it doesn't require any additional configuration to fetch GitHub issues.
 
-### Jira Integration 💎
+## Jira Integration 💎
 
 We support both Jira Cloud and Jira Server/Data Center.
-To integrate with Jira, you can link your PR to a ticket using either of these methods:
 
-**Method 1: Description Reference:**
-
-Include a ticket reference in your PR description using either the complete URL format https://<JIRA_ORG>.atlassian.net/browse/ISSUE-123 or the shortened ticket ID ISSUE-123.
-
-**Method 2: Branch Name Detection:**
-
-Name your branch with the ticket ID as a prefix (e.g., `ISSUE-123-feature-description` or `ISSUE-123/feature-description`).
-
-!!! note "Jira Base URL"
-    For shortened ticket IDs or branch detection (method 2), you must configure the Jira base URL in your configuration file under the [jira] section:
-
-    ```toml
-    [jira]
-    jira_base_url = "https://<JIRA_ORG>.atlassian.net"
-    ```
-
-#### Jira Cloud 💎
+### Jira Cloud
 There are two ways to authenticate with Jira Cloud:
 
 **1) Jira App Authentication**
@@ -95,7 +77,7 @@ Installation steps:
 2. After installing the app, you will be redirected to the Qodo Merge registration page. and you will see a success message.<br>
 ![Jira Cloud App success message](https://www.qodo.ai/images/pr_agent/jira_app_success.png){width=384}
 
-3. Now you can use the Jira integration in Qodo Merge PR Agent.
+3. Now Qodo Merge will be able to fetch Jira ticket context for your PRs.
 
 **2) Email/Token Authentication**
 
@@ -120,9 +102,70 @@ jira_api_email = "YOUR_EMAIL"
 ```
 
 
-#### Jira Server/Data Center 💎
+### Jira Data Center/Server
 
-Currently, we only support the Personal Access Token (PAT) Authentication method.
+[//]: # ()
+[//]: # (##### Local App Authentication &#40;For Qodo Merge On-Premise Customers&#41;)
+
+[//]: # ()
+[//]: # (##### 1. Step 1: Set up an application link in Jira Data Center/Server)
+
+[//]: # (* Go to Jira Administration > Applications > Application Links > Click on `Create link`)
+
+[//]: # ()
+[//]: # (![application links]&#40;https://www.qodo.ai/images/pr_agent/jira_app_links.png&#41;{width=384})
+
+[//]: # (* Choose `External application` and set the direction to `Incoming` and then click `Continue`)
+
+[//]: # ()
+[//]: # (![external application]&#40;https://www.qodo.ai/images/pr_agent/jira_create_link.png&#41;{width=256})
+
+[//]: # (* In the following screen, enter the following details:)
+
+[//]: # (    * Name: `Qodo Merge`)
+
+[//]: # (    * Redirect URL: Enter your Qodo Merge URL followed  `https://{QODO_MERGE_ENDPOINT}/register_ticket_provider`)
+
+[//]: # (    * Permission: Select `Read`)
+
+[//]: # (    * Click `Save`)
+
+[//]: # ()
+[//]: # (![external application details]&#40;https://www.qodo.ai/images/pr_agent/jira_fill_app_link.png&#41;{width=384})
+
+[//]: # (* Copy the `Client ID` and `Client secret` and set them in your `.secrets` file:)
+
+[//]: # ()
+[//]: # (![client id and secret]&#40;https://www.qodo.ai/images/pr_agent/jira_app_credentionals.png&#41;{width=256})
+
+[//]: # (```toml)
+
+[//]: # ([jira])
+
+[//]: # (jira_app_secret = "...")
+
+[//]: # (jira_client_id = "...")
+
+[//]: # (```)
+
+[//]: # ()
+[//]: # (##### 2. Step 2: Authenticate with Jira Data Center/Server)
+
+[//]: # (* Open this URL in your browser: `https://{QODO_MERGE_ENDPOINT}/jira_auth`)
+
+[//]: # (* Click on link)
+
+[//]: # ()
+[//]: # (![jira auth success]&#40;https://www.qodo.ai/images/pr_agent/jira_auth_page.png&#41;{width=384})
+
+[//]: # ()
+[//]: # (* You will be redirected to Jira Data Center/Server, click `Allow`)
+
+[//]: # (* You will be redirected back to Qodo Merge and you will see a success message.)
+
+
+[//]: # (Personal Access Token &#40;PAT&#41; Authentication)
+Currently, JIRA integration for Data Center/Server is available via Personal Access Token (PAT) Authentication method 
 
 1. Create a [Personal Access Token (PAT)](https://confluence.atlassian.com/enterprise/using-personal-access-tokens-1026032365.html) in your Jira account
 2. In your Configuration file/Environment variables/Secrets file, add the following lines:
@@ -132,3 +175,67 @@ Currently, we only support the Personal Access Token (PAT) Authentication method
 jira_base_url = "YOUR_JIRA_BASE_URL" # e.g. https://jira.example.com
 jira_api_token = "YOUR_API_TOKEN"
 ```
+
+#### Validating PAT token via Python script
+
+If you are facing issues retrieving tickets in Qodo Merge with PAT token, you can validate the flow using a Python script. 
+This following steps will help you check if the token is working correctly, and if you can access the Jira ticket details:
+
+1. run `pip install jira==3.8.0`
+
+2. run the following Python script (after replacing the placeholders with your actual values):
+
+??? example "Script to validate PAT token"
+
+    ```python
+    from jira import JIRA
+    
+    
+    if __name__ == "__main__":
+        try:
+            # Jira server URL
+            server = "https://..."
+            # Jira PAT token
+            token_auth = "..."
+            # Jira ticket code (e.g. "PROJ-123")
+            ticket_id = "..."
+    
+            print("Initializing JiraServerTicketProvider with JIRA server")
+            # Initialize JIRA client
+            jira = JIRA(
+                server=server,
+                token_auth=token_auth,
+                timeout=30
+            )
+            if jira:
+                print(f"JIRA client initialized successfully")
+            else:
+                print("Error initializing JIRA client")
+    
+            # Fetch ticket details
+            ticket = jira.issue(ticket_id)
+            print(f"Ticket title: {ticket.fields.summary}")
+    
+        except Exception as e:
+            print(f"Error fetching JIRA ticket details: {e}")
+    ```
+
+### How to link a PR to a Jira ticket
+
+To integrate with Jira, you can link your PR to a ticket using either of these methods:
+
+**Method 1: Description Reference:**
+
+Include a ticket reference in your PR description using either the complete URL format https://<JIRA_ORG>.atlassian.net/browse/ISSUE-123 or the shortened ticket ID ISSUE-123.
+
+**Method 2: Branch Name Detection:**
+
+Name your branch with the ticket ID as a prefix (e.g., `ISSUE-123-feature-description` or `ISSUE-123/feature-description`).
+
+!!! note "Jira Base URL"
+    For shortened ticket IDs or branch detection (method 2 for JIRA cloud), you must configure the Jira base URL in your configuration file under the [jira] section:
+
+    ```toml
+    [jira]
+    jira_base_url = "https://<JIRA_ORG>.atlassian.net"
+    ```

docs/docs/core-abilities/index.md

@@ -1,16 +1,18 @@
 # Core Abilities
 Qodo Merge utilizes a variety of core abilities to provide a comprehensive and efficient code review experience. These abilities include:
 
-- [Fetching ticket context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
-- [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)
+- [Auto best practices](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices/)
+- [Pull request benchmark](https://qodo-merge-docs.qodo.ai/finetuning_benchmark/)
+- [Code validation](https://qodo-merge-docs.qodo.ai/core-abilities/code_validation/)
+- [Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)
 - [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)
-- [Self-reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)
+- [Fetching ticket context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/)
 - [Impact evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/)
 - [Interactivity](https://qodo-merge-docs.qodo.ai/core-abilities/interactivity/)
-- [Compression strategy](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)
-- [Code-oriented YAML](https://qodo-merge-docs.qodo.ai/core-abilities/code_oriented_yaml/)
+- [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)
+- [RAG context enrichment](https://qodo-merge-docs.qodo.ai/core-abilities/rag_context_enrichment/)
+- [Self-reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)
 - [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/)
-- [Code fine-tuning benchmark](https://qodo-merge-docs.qodo.ai/finetuning_benchmark/)
 
 ## Blogs
 
@@ -18,6 +20,7 @@ Here are some additional technical blogs from Qodo, that delve deeper into the c
 These resources provide more comprehensive insights into leveraging LLMs for software development.
 
 ### Code Generation and LLMs
+- [Effective AI code suggestions: less is more](https://www.qodo.ai/blog/effective-code-suggestions-llms-less-is-more/)
 - [State-of-the-art Code Generation with AlphaCodium – From Prompt Engineering to Flow Engineering](https://www.qodo.ai/blog/qodoflow-state-of-the-art-code-generation-for-code-contests/)
 - [RAG for a Codebase with 10k Repos](https://www.qodo.ai/blog/rag-for-large-scale-code-repos/)
 

docs/docs/core-abilities/interactivity.md

@@ -1,2 +1,43 @@
-## Interactive invocation 💎
-TBD
+# Interactivity
+
+`Supported Git Platforms: GitHub, GitLab`
+
+## Overview
+
+Qodo Merge transforms static code reviews into interactive experiences by enabling direct actions from pull request (PR) comments.
+Developers can immediately trigger actions and apply changes with simple checkbox clicks. 
+
+This focused workflow maintains context while dramatically reducing the time between PR creation and final merge.
+The approach eliminates manual steps, provides clear visual indicators, and creates immediate feedback loops all within the same interface.
+
+## Key Interactive Features
+
+### 1\. Interactive `/improve` Tool
+
+The [`/improve`](https://qodo-merge-docs.qodo.ai/tools/improve/) command delivers a comprehensive interactive experience:
+
+- _**Apply this suggestion**_: Clicking this checkbox instantly converts a suggestion into a committable code change. When committed to the PR, changes made to code that was flagged for improvement will be marked with a check mark, allowing developers to easily track and review implemented recommendations.
+
+- _**More**_: Triggers additional suggestions generation while keeping each suggestion focused and relevant as the original set
+
+- _**Update**_: Triggers a re-analysis of the code, providing updated suggestions based on the latest changes
+
+- _**Author self-review**_: Interactive acknowledgment that developers have opened and reviewed collapsed suggestions
+
+
+###  2\. Interactive `/analyze` Tool
+
+The [`/analyze`](https://qodo-merge-docs.qodo.ai/tools/analyze/) command provides component-level analysis with interactive options for each identified code component:
+
+- Interactive checkboxes to generate tests, documentation, and code suggestions for specific components
+
+- On-demand similar code search that activates when a checkbox is clicked
+
+- Component-specific actions that trigger only for the selected elements, providing focused assistance
+
+
+###  3\. Interactive `/help` Tool
+
+The [`/help`](https://qodo-merge-docs.qodo.ai/tools/help/) command not only lists available tools and their descriptions but also enables immediate tool invocation through interactive checkboxes. 
+When a user checks a tool's checkbox, Qodo Merge instantly triggers that tool without requiring additional commands. 
+This transforms the standard help menu into an interactive launch pad for all Qodo Merge capabilities, eliminating context switching by keeping developers within their PR workflow.

docs/docs/core-abilities/metadata.md

@@ -1,5 +1,5 @@
 ## Local and global metadata injection with multi-stage analysis
-(1)
+1\.
 Qodo Merge initially retrieves for each PR the following data:
 
 - PR title and branch name
@@ -11,7 +11,7 @@ Qodo Merge initially retrieves for each PR the following data:
 !!! tip "Tip: Organization-level metadata"
     In addition to the inputs above, Qodo Merge can incorporate supplementary preferences provided by the user, like [`extra_instructions` and `organization best practices`](https://qodo-merge-docs.qodo.ai/tools/improve/#extra-instructions-and-best-practices). This information can be used to enhance the PR analysis.
 
-(2)
+2\.
 By default, the first command that Qodo Merge executes is [`describe`](https://qodo-merge-docs.qodo.ai/tools/describe/), which generates three types of outputs:
 
 - PR Type (e.g. bug fix, feature, refactor, etc)
@@ -32,14 +32,14 @@ For example, when generating code suggestions for different files, Qodo Merge ca
 
 @@ ... @@ def func1():
 __new hunk__
-11  unchanged code line0 in the PR
-12  unchanged code line1 in the PR
-13 +new code line2 added in the PR
-14  unchanged code line3 in the PR
+11  unchanged code line0
+12  unchanged code line1
+13 +new code line2 added
+14  unchanged code line3
 __old hunk__
  unchanged code line0
  unchanged code line1
--old code line2 removed in the PR
+-old code line2 removed
  unchanged code line3
 
 @@ ... @@ def func2():
@@ -49,8 +49,8 @@ __old hunk__
 ...
 ```
 
-(3) The entire PR files that were retrieved are also used to expand and enhance the PR context (see [Dynamic Context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)).
+3\. The entire PR files that were retrieved are also used to expand and enhance the PR context (see [Dynamic Context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)).
 
 
-(4) All the metadata described above represents several level of cumulative analysis - ranging from hunk level, to file level, to PR level, to organization level.
+4\. All the metadata described above represents several level of cumulative analysis - ranging from hunk level, to file level, to PR level, to organization level.
 This comprehensive approach enables Qodo Merge AI models to generate more precise and contextually relevant suggestions and feedback.

docs/docs/core-abilities/rag_context_enrichment.md

@@ -0,0 +1,78 @@
+# RAG Context Enrichment 💎
+
+`Supported Git Platforms: GitHub`
+
+!!! info "Prerequisites"
+    - RAG is available only for Qodo enterprise plan users, with single tenant or on-premises setup.
+    - Database setup and codebase indexing must be completed before proceeding. [Contact support](https://www.qodo.ai/contact/) for more information.
+
+
+## Overview
+
+### What is RAG Context Enrichment?
+
+A feature that enhances AI analysis by retrieving and referencing relevant code patterns from your project, enabling context-aware insights during code reviews.
+
+### How does RAG Context Enrichment work?
+
+Using Retrieval-Augmented Generation (RAG), it searches your configured repositories for contextually relevant code segments, enriching pull request (PR) insights and accelerating review accuracy.
+
+
+## Getting started
+
+### Configuration options
+
+In order to enable the RAG feature, add the following lines to your configuration file:
+``` toml
+[rag_arguments]
+enable_rag=true
+```
+
+!!! example "RAG Arguments Options"
+
+    <table>
+      <tr>
+        <td><b>enable_rag</b></td>
+        <td>If set to true, repository enrichment using RAG will be enabled. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>rag_repo_list</b></td>
+        <td>A list of repositories that will be used by the semantic search for RAG. Use `['all']` to consider the entire codebase or a select list of repositories, for example: ['my-org/my-repo', ...]. Default: the repository from which the PR was opened.</td>
+      </tr>
+    </table>
+
+### Applications
+
+#### 1\. The `/review` Tool
+
+The [`/review`](https://qodo-merge-docs.qodo.ai/tools/review/) tool offers the _Focus area from RAG data_ which contains feedback based on the RAG references analysis. 
+The complete list of references found relevant to the PR will be shown in the _References_ section, helping developers understand the broader context by exploring the provided references.
+
+![References](https://codium.ai/images/pr_agent/rag_review.png){width=640}
+
+#### 2\. The `/implement` Tool
+
+The [`/implement`](https://qodo-merge-docs.qodo.ai/tools/implement/) tool utilizes the RAG feature to provide comprehensive context of the repository codebase, allowing it to generate more refined code output.
+The _References_ section contains links to the content used to support the code generation.
+
+![References](https://codium.ai/images/pr_agent/rag_implement.png){width=640}
+
+#### 3\. The `/ask` Tool
+
+The [`/ask`](https://qodo-merge-docs.qodo.ai/tools/ask/) tool can access broader repository context through the RAG feature when answering questions that go beyond the PR scope alone.
+The _References_ section displays the additional repository content consulted to formulate the answer.
+
+![References](https://codium.ai/images/pr_agent/rag_ask.png){width=640}
+
+
+## Limitations
+
+### Querying the codebase presents significant challenges
+- **Search Method**: RAG uses natural language queries to find semantically relevant code sections
+- **Result Quality**: No guarantee that RAG results will be useful for all queries
+- **Scope Recommendation**: To reduce noise, focus on the PR repository rather than searching across multiple repositories
+
+### This feature has several requirements and restrictions
+- **Codebase**: Must be properly indexed for search functionality
+- **Security**: Requires secure and private indexed codebase implementation
+- **Deployment**: Only available for Qodo Merge Enterprise plan using single tenant or on-premises setup

docs/docs/faq/index.md

@@ -1,6 +1,6 @@
 # FAQ
 
-??? note "Question: Can Qodo Merge serve as a substitute for a human reviewer?"
+??? note "Q: Can Qodo Merge serve as a substitute for a human reviewer?"
     #### Answer:<span style="display:none;">1</span>
 
     Qodo Merge is designed to assist, not replace, human reviewers.
@@ -12,7 +12,7 @@
 
     1. Preserves user's original PR header
     2. Places user's description above the AI-generated PR description
-    3. Cannot approve PRs; approval remains reviewer's responsibility
+    3. Won't approve PRs; approval remains reviewer's responsibility
     4. The code suggestions are optional, and aim to:
         - Encourage self-review and self-reflection
         - Highlight potential bugs or oversights
@@ -22,15 +22,15 @@
 
 ___
 
-??? note "Question: I received an incorrect or irrelevant suggestion. Why?"
+??? note "Q: I received an incorrect or irrelevant suggestion. Why?"
 
     #### Answer:<span style="display:none;">2</span>
 
-    - Modern AI models, like Claude 3.5 Sonnet and GPT-4, are improving rapidly but remain imperfect. Users should critically evaluate all suggestions rather than accepting them automatically.
-    - AI errors are rare, but possible. A main value from reviewing the code suggestions lies in their high probability of catching **mistakes or bugs made by the PR author**. We believe it's worth spending 30-60 seconds reviewing suggestions, even if some aren't relevant, as this practice can enhances code quality and prevent bugs in production.
+    - Modern AI models, like Claude Sonnet and GPT-4, are improving rapidly but remain imperfect. Users should critically evaluate all suggestions rather than accepting them automatically.
+    - AI errors are rare, but possible. A main value from reviewing the code suggestions lies in their high probability of catching **mistakes or bugs made by the PR author**. We believe it's worth spending 30-60 seconds reviewing suggestions, even if some aren't relevant, as this practice can enhance code quality and prevent bugs in production.
 
 
-    - The hierarchical structure of the suggestions is designed to help the user to _quickly_ understand them, and to decide which ones are relevant and which are not:
+    - The hierarchical structure of the suggestions is designed to help the user _quickly_ understand them, and to decide which ones are relevant and which are not:
 
         - Only if the `Category` header is relevant, the user should move to the summarized suggestion description.
         - Only if the summarized suggestion description is relevant, the user should click on the collapsible, to read the full suggestion description with a code preview example.
@@ -40,14 +40,14 @@ ___
 
 ___
 
-??? note "Question: How can I get more tailored suggestions?"
+??? note "Q: How can I get more tailored suggestions?"
     #### Answer:<span style="display:none;">3</span>
 
     See [here](https://qodo-merge-docs.qodo.ai/tools/improve/#extra-instructions-and-best-practices) for more information on how to use the `extra_instructions` and `best_practices` configuration options, to guide the model to more tailored suggestions.
 
 ___
 
-??? note "Question: Will you store my code ? Are you using my code to train models?"
+??? note "Q: Will you store my code? Are you using my code to train models?"
     #### Answer:<span style="display:none;">4</span>
 
     No. Qodo Merge strict privacy policy ensures that your code is not stored or used for training purposes.
@@ -56,12 +56,35 @@ ___
 
 ___
 
-??? note "Question: Can I use my own LLM keys with Qodo Merge?"
+??? note "Q: Can I use my own LLM keys with Qodo Merge?"
     #### Answer:<span style="display:none;">5</span>
 
-    When you self-host, you use your own keys.
+    When you self-host the [open-source](https://github.com/Codium-ai/pr-agent) version, you use your own keys.
 
-    Qodo Merge Pro with SaaS deployment is a hosted version of Qodo Merge, where Qodo manages the infrastructure and the keys.
+    Qodo Merge with SaaS deployment is a hosted version of Qodo Merge, where Qodo manages the infrastructure and the keys.
     For enterprise customers, on-prem deployment is also available. [Contact us](https://www.codium.ai/contact/#pricing) for more information.
+___
+
+??? note "Q: Can Qodo Merge review draft/offline PRs?"
+    #### Answer:<span style="display:none;">5</span>
+
+    Yes. While Qodo Merge won't automatically review draft PRs, you can still get feedback by manually requesting it through [online commenting](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#online-usage).
+
+    For active PRs, you can customize the automatic feedback settings [here](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#qodo-merge-automatic-feedback) to match your team's workflow.
+___
+
+??? note "Q: Can the 'Review effort' feedback be calibrated or customized?"
+    #### Answer:<span style="display:none;">5</span>
+
+    Yes, you can customize review effort estimates using the `extra_instructions` configuration option (see [documentation](https://qodo-merge-docs.qodo.ai/tools/review/#configuration-options)).
+    
+    Example mapping:
+
+    - Effort 1: < 30 minutes review time
+    - Effort 2: 30-60 minutes review time
+    - Effort 3: 60-90 minutes review time
+    - ...
+    
+    Note: The effort levels (1-5) are primarily meant for _comparative_ purposes, helping teams prioritize reviewing smaller PRs first. The actual review duration may vary, as the focus is on providing consistent relative effort estimates.
 
 ___

docs/docs/finetuning_benchmark/index.md

@@ -1,10 +1,10 @@
-# Qodo Merge Code Fine-tuning Benchmark
+# Qodo Merge Pull Request Benchmark
 
-On coding tasks, the gap between open-source models and top closed-source models such as GPT4 is significant.
+On coding tasks, the gap between open-source models and top closed-source models such as Claude and GPT is significant.
 <br>
 In practice, open-source models are unsuitable for most real-world code tasks, and require further fine-tuning to produce acceptable results.
 
-_Qodo Merge fine-tuning benchmark_ aims to benchmark open-source models on their ability to be fine-tuned for a coding task.
+_Qodo Merge pull request benchmark_ aims to benchmark models on their ability to be fine-tuned for a coding task.
 Specifically, we chose to fine-tune open-source models on the task of analyzing a pull request, and providing useful feedback and code suggestions.
 
 Here are the results:
@@ -49,7 +49,7 @@ Here are the results:
 - **The best small model** - For small 7B code-dedicated models, the gaps when fine-tuning are much larger. **CodeQWEN 1.5-7B** is by far the best model for fine-tuning.
 - **Base vs. instruct** - For the top model (deepseek), we saw small advantage when starting from the instruct version. However, we recommend testing both versions on each specific task, as the base model is generally considered more suitable for fine-tuning.
 
-## The dataset
+## Dataset
 
 ### Training dataset
 
@@ -68,7 +68,7 @@ Here are the prompts, and example outputs, used as input-output pairs to fine-tu
 
 ### Evaluation dataset
 
-- For each tool, we aggregated 100 additional examples to be used for evaluation. These examples were not used in the training dataset, and were manually selected to represent diverse real-world use-cases.
+- For each tool, we aggregated 200 additional examples to be used for evaluation. These examples were not used in the training dataset, and were manually selected to represent diverse real-world use-cases.
 - For each test example, we generated two responses: one from the fine-tuned model, and one from the best code model in the world, `gpt-4-turbo-2024-04-09`.
 
 - We used a third LLM to judge which response better answers the prompt, and will likely be perceived by a human as better response.
@@ -91,3 +91,11 @@ why: |
   actionable suggestions, such as changing variable names and adding comments, which are less
   critical for immediate code improvement."
 ```
+
+## Comparing Top Closed-Source Models
+
+Another application of the Pull Request Benchmark is comparing leading closed-source models to determine which performs better at analyzing pull request code.
+
+The evaluation methodology resembles the approach used for evaluating fine-tuned models:
+- We ran each model across 200 diverse pull requests, asking them to generate code suggestions using Qodo Merge's `improve` tool
+- A third top model served as judge to determine which response better fulfilled the prompt and would likely be perceived as superior by human users

docs/docs/index.md

@@ -1,15 +1,17 @@
 # Overview
 
-Qodo Merge is an open-source tool to help efficiently review and handle pull requests.
+[PR-Agent](https://github.com/Codium-ai/pr-agent) is an open-source tool to help efficiently review and handle pull requests. 
+Qodo Merge is a hosted version of PR-Agent, designed for companies and teams that require additional features and capabilities
 
 - See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
 
-- See the [Usage Guide](./usage-guide/index.md) for instructions on running the Qodo Merge commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
+- See the [Usage Guide](./usage-guide/index.md) for instructions on running commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
 
 - See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
 
+- See the [Video Tutorials](https://www.youtube.com/playlist?list=PLRTpyDOSgbwFMA_VBeKMnPLaaZKwjGBFT) for practical demonstrations on how to use the tools.
 
-## Qodo Merge Docs Smart Search
+## Docs Smart Search
 
 To search the documentation site using natural language:
 
@@ -18,50 +20,54 @@ To search the documentation site using natural language:
    - A pull request where Qodo Merge is installed
    - A [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat)
 
-2) Qodo Merge will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
+2) The bot will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
 
 
-## Qodo Merge Features
+## Features
 
-Qodo Merge offers extensive pull request functionalities across various git providers.
+PR-Agent and Qodo Merge offers extensive pull request functionalities across various git providers:
 
-|       |                                                                                                         | GitHub             | GitLab             | Bitbucket          | Azure DevOps |
-|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:--------------------:|:------------:|
-| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                                                                                | ✅ | ✅ | ✅ |      ✅       |
-|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | ⮑ [Ask on code lines](https://pr-agent-docs.codium.ai/tools/ask#ask-lines)                              | ✅ | ✅ |                    |              |
-|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎  | ✅ | ✅ |  ✅                  |   |
-|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎  | ✅ |  |                    |   |
-|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎  | ✅ | ✅ |                    |   |
-|       | [CI Feedback](https://pr-agent-docs.codium.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |                    |              |
-|       | [PR Documentation](https://pr-agent-docs.codium.ai/tools/documentation/) 💎                         | ✅ | ✅ |                   |              |
-|       | [Custom Labels](https://pr-agent-docs.codium.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |                    |              |
-|       | [Analyze](https://pr-agent-docs.codium.ai/tools/analyze/) 💎                                            | ✅ | ✅ |                    |              |
-|       | [Similar Code](https://pr-agent-docs.codium.ai/tools/similar_code/) 💎                                  | ✅ |                    |                    |              |
-|       | [Custom Prompt](https://pr-agent-docs.codium.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ | ✅ |              |
-|       | [Test](https://pr-agent-docs.codium.ai/tools/test/) 💎                                                  | ✅ | ✅ |                    |              |
-|       |                                                                                                         |                    |                    |                    |              |
-| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                                                                                                     | ✅ | ✅ | ✅ |      ✅       |
-|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)                                                                                           | ✅ | ✅ | ✅ |      ✅       |
-|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                                                                             | ✅ |                    |                    |              |
-|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                                                                                                 | ✅ |✅| ✅ |✅|
-|       |                                                                                                         |                    |                    |                    |              |
-| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                                                                  | ✅ | ✅ | ✅ |      ✅       |
-|       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ | ✅ |      ✅       |
-|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                                                                                 | ✅ | ✅ | ✅ |      ✅       |
-|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Self reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)          | ✅ | ✅ | ✅ | ✅             |
-|       | [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/) 💎         | ✅ | ✅ | ✅ |              |
-|       | [Global and wiki configurations](https://pr-agent-docs.codium.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ | ✅ |              |
-|       | [PR interactive actions](https://www.codium.ai/images/pr_agent/pr-actions.mp4) 💎                       | ✅ |        ✅           |                    |              |
-|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎  | ✅ | ✅ |                    |   |
+|       |                                                                                                         | GitHub             | GitLab             | Bitbucket | Azure DevOps |
+|-------|---------------------------------------------------------------------------------------------------------|:--------------------:|:--------------------:|:---------:|:------------:|
+| TOOLS | [Review](https://qodo-merge-docs.qodo.ai/tools/review/)                                                 | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Describe](https://qodo-merge-docs.qodo.ai/tools/describe/)                                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Improve](https://qodo-merge-docs.qodo.ai/tools/improve/)                                               | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Ask](https://qodo-merge-docs.qodo.ai/tools/ask/)                                                       | ✅ | ✅ |     ✅     |      ✅       |
+|       | ⮑ [Ask on code lines](https://qodo-merge-docs.qodo.ai/tools/ask/#ask-lines)                             | ✅ | ✅ |           |              |
+|       | [Update CHANGELOG](https://qodo-merge-docs.qodo.ai/tools/update_changelog/)                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Help Docs](https://qodo-merge-docs.qodo.ai/tools/help_docs/?h=auto#auto-approval)                      |   ✅    |   ✅    |   ✅        |            |
+|       | [Ticket Context](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/) 💎            | ✅ | ✅ |     ✅     |   |
+|       | [Utilizing Best Practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 💎            | ✅ | ✅ |     ✅     |   |
+|       | [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) 💎                        | ✅ |  |           |   |
+|       | [Suggestion Tracking](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking) 💎            | ✅ | ✅ |           |   |
+|       | [CI Feedback](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/) 💎                                    | ✅ |                    |           |              |
+|       | [PR Documentation](https://qodo-merge-docs.qodo.ai/tools/documentation/) 💎                             | ✅ | ✅ |           |              |
+|       | [Custom Labels](https://qodo-merge-docs.qodo.ai/tools/custom_labels/) 💎                                | ✅ | ✅ |           |              |
+|       | [Analyze](https://qodo-merge-docs.qodo.ai/tools/analyze/) 💎                                            | ✅ | ✅ |           |              |
+|       | [Similar Code](https://qodo-merge-docs.qodo.ai/tools/similar_code/) 💎                                  | ✅ |                    |           |              |
+|       | [Custom Prompt](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/) 💎                                | ✅ | ✅ |     ✅     |              |
+|       | [Test](https://qodo-merge-docs.qodo.ai/tools/test/) 💎                                                  | ✅ | ✅ |           |              |
+|       | [Implement](https://qodo-merge-docs.qodo.ai/tools/implement/) 💎                                        | ✅ | ✅ |     ✅     |              |
+|       | [Auto-Approve](https://qodo-merge-docs.qodo.ai/tools/improve/?h=auto#auto-approval) 💎                  |   ✅    |   ✅    |   ✅        |            |
+|       |                                                                                                         |                    |                    |           |              |
+| USAGE | [CLI](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#local-repo-cli)                | ✅ | ✅ |     ✅     |      ✅       |
+|       | [App / webhook](https://qodo-merge-docs.qodo.ai/usage-guide/automations_and_usage/#github-app)          | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Tagging bot](https://github.com/Codium-ai/pr-agent#try-it-now)                                         | ✅ |                    |           |              |
+|       | [Actions](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action)                  | ✅ |✅|     ✅     |✅|
+|       |                                                                                                         |                    |                    |           |              |
+| CORE  | [PR compression](https://qodo-merge-docs.qodo.ai/core-abilities/compression_strategy/)                  | ✅ | ✅ |     ✅     |      ✅       |
+|       | Adaptive and token-aware file patch fitting                                                             | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Multiple models support](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/)                | ✅ | ✅ |     ✅     |      ✅       |
+|       | [Local and global metadata](https://qodo-merge-docs.qodo.ai/core-abilities/metadata/)                   | ✅ | ✅ |     ✅     | ✅             |
+|       | [Dynamic context](https://qodo-merge-docs.qodo.ai/core-abilities/dynamic_context/)                      | ✅ | ✅ |     ✅     | ✅             |
+|       | [Self reflection](https://qodo-merge-docs.qodo.ai/core-abilities/self_reflection/)                      | ✅ | ✅ |     ✅     | ✅             |
+|       | [Static code analysis](https://qodo-merge-docs.qodo.ai/core-abilities/static_code_analysis/) 💎         | ✅ | ✅ |           |              |
+|       | [Global and wiki configurations](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) 💎 | ✅ | ✅ |     ✅     |              |
+|       | [PR interactive actions](https://www.qodo.ai/images/pr_agent/pr-actions.mp4) 💎                         | ✅ |        ✅           |           |              |
+|       | [Impact Evaluation](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) 💎               | ✅ | ✅ |           |   |
 
-💎 marks a feature available only in [Qodo Merge Pro](https://www.qodo.ai/pricing/){:target="_blank"}
+!!! note "💎 means Qodo Merge only"
+      All along the documentation, 💎 marks a feature available only in [Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"}, and not in the open-source version.
 
 
 ## Example Results
@@ -97,4 +103,4 @@ The following diagram illustrates Qodo Merge tools and their flow:
 
 ![Qodo Merge Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
 
-Check out the [core abilities](core-abilities/index.md) page for a comprehensive overview of the variety of core abilities used by Qodo Merge.
+Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/installation/azure.md

@@ -1,5 +1,5 @@
 ## Azure DevOps Pipeline
-You can use a pre-built Action Docker image to run Qodo Merge as an Azure devops pipeline.
+You can use a pre-built Action Docker image to run PR-Agent as an Azure devops pipeline.
 add the following file to your repository under `azure-pipelines.yml`:
 ```yaml
 # Opt out of CI triggers
@@ -52,7 +52,7 @@ stages:
 This script will run Qodo Merge on every new merge request, with the `improve`, `review`, and `describe` commands.
 Note that you need to export the `azure_devops__pat` and `OPENAI_KEY` variables in the Azure DevOps pipeline settings (Pipelines -> Library -> + Variable group):
 
-![Qodo Merge Pro](https://codium.ai/images/pr_agent/azure_devops_pipeline_secrets.png){width=468}
+![Qodo Merge](https://codium.ai/images/pr_agent/azure_devops_pipeline_secrets.png){width=468}
 
 Make sure to give pipeline permissions to the `pr_agent` variable group.
 
@@ -80,7 +80,7 @@ org = "https://dev.azure.com/YOUR_ORGANIZATION/"
 # pat = "YOUR_PAT_TOKEN" needed only if using PAT for authentication
 ```
 
-### Azure DevOps Webhook
+## Azure DevOps Webhook
 
 To trigger from an Azure webhook, you need to manually [add a webhook](https://learn.microsoft.com/en-us/azure/devops/service-hooks/services/webhooks?view=azure-devops).
 Use the "Pull request created" type to trigger a review, or "Pull request commented on" to trigger any supported comment with /<command> <args> comment on the relevant PR. Note that for the "Pull request commented on" trigger, only API v2.0 is supported.

docs/docs/installation/bitbucket.md

@@ -1,37 +1,33 @@
 ## Run as a Bitbucket Pipeline
 
-
-You can use the Bitbucket Pipeline system to run Qodo Merge on every pull request open or update.
+You can use the Bitbucket Pipeline system to run PR-Agent on every pull request open or update.
 
 1. Add the following file in your repository bitbucket-pipelines.yml
 
 ```yaml
 pipelines:
-    pull-requests:
-      '**':
-        - step:
-            name: PR Agent Review
-            image: python:3.10
-            services:
-              - docker
-            script:
-              - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=https://bitbucket.org/$BITBUCKET_WORKSPACE/$BITBUCKET_REPO_SLUG/pull-requests/$BITBUCKET_PR_ID review
+  pull-requests:
+    "**":
+      - step:
+          name: PR Agent Review
+          image: python:3.12
+          services:
+            - docker
+          script:
+            - docker run -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=https://bitbucket.org/$BITBUCKET_WORKSPACE/$BITBUCKET_REPO_SLUG/pull-requests/$BITBUCKET_PR_ID review
 ```
 
 2. Add the following secure variables to your repository under Repository settings > Pipelines > Repository variables.
-OPENAI_API_KEY: `<your key>`
-BITBUCKET_BEARER_TOKEN: `<your token>`
+   OPENAI_API_KEY: `<your key>`
+   BITBUCKET.AUTH_TYPE: `basic` or `bearer` (default is `bearer`)
+   BITBUCKET.BEARER_TOKEN: `<your token>` (required when auth_type is bearer)
+   BITBUCKET.BASIC_TOKEN: `<your token>` (required when auth_type is basic)
 
 You can get a Bitbucket token for your repository by following Repository Settings -> Security -> Access Tokens.
+For basic auth, you can generate a base64 encoded token from your username:password combination.
 
 Note that comments on a PR are not supported in Bitbucket Pipeline.
 
-
-## Run using CodiumAI-hosted Bitbucket app 💎
-
-Please contact visit [Qodo Merge Pro](https://www.codium.ai/pricing/) if you're interested in a hosted BitBucket app solution that provides full functionality including PR reviews and comment handling. It's based on the [bitbucket_app.py](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/git_providers/bitbucket_provider.py) implementation.
-
-
 ## Bitbucket Server and Data Center
 
 Login into your on-prem instance of Bitbucket with your service account username and password.
@@ -52,13 +48,15 @@ git_provider="bitbucket_server"
 ```
 
 and pass the Pull request URL:
+
 ```shell
 python cli.py --pr_url https://git.onpreminstanceofbitbucket.com/projects/PROJECT/repos/REPO/pull-requests/1 review
 ```
 
 ### Run it as service
 
-To run Qodo Merge as webhook, build the docker image:
+To run PR-Agent as webhook, build the docker image:
+
 ```
 docker build . -t codiumai/pr-agent:bitbucket_server_webhook --target bitbucket_server_webhook -f docker/Dockerfile
 docker push codiumai/pr-agent:bitbucket_server_webhook  # Push to your Docker repository

docs/docs/installation/github.md

@@ -1,6 +1,6 @@
 ## Run as a GitHub Action
 
-You can use our pre-built Github Action Docker image to run Qodo Merge as a Github Action.
+You can use our pre-built Github Action Docker image to run PR-Agent as a Github Action.
 
 1) Add the following file to your repository under `.github/workflows/pr_agent.yml`:
 
@@ -21,7 +21,7 @@ jobs:
     steps:
       - name: PR Agent action step
         id: pragent
-        uses: Codium-ai/pr-agent@main
+        uses: qodo-ai/pr-agent@main
         env:
           OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

docs/docs/installation/gitlab.md

@@ -1,5 +1,5 @@
 ## Run as a GitLab Pipeline
-You can use a pre-built Action Docker image to run Qodo Merge as a GitLab pipeline. This is a simple way to get started with Qodo Merge without setting up your own server.
+You can use a pre-built Action Docker image to run PR-Agent as a GitLab pipeline. This is a simple way to get started with Qodo Merge without setting up your own server.
 
 (1) Add the following file to your repository under `.gitlab-ci.yml`:
 ```yaml
@@ -43,36 +43,47 @@ Note that if your base branches are not protected, don't set the variables as `p
 
 ## Run a GitLab webhook server
 
-1. From the GitLab workspace or group, create an access token with "Reporter" role ("Developer" if using Pro version of the agent) and "api" scope.
+1. In GitLab create a new user and give it "Reporter" role ("Developer" if using Pro version of the agent) for the intended group or project.
 
-2. Generate a random secret for your app, and save it for later. For example, you can use:
+2. For the user from step 1. generate a `personal_access_token` with `api` access.
+
+3. Generate a random secret for your app, and save it for later (`shared_secret`). For example, you can use:
 
 ```
-WEBHOOK_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
+SHARED_SECRET=$(python -c "import secrets; print(secrets.token_hex(10))")
 ```
 
-3. Clone this repository:
+4. Clone this repository:
 
 ```
-git clone https://github.com/Codium-ai/pr-agent.git
+git clone https://github.com/qodo-ai/pr-agent.git
 ```
 
-4. Prepare variables and secrets. Skip this step if you plan on settings these as environment variables when running the agent:
+5. Prepare variables and secrets. Skip this step if you plan on setting these as environment variables when running the agent:
   1. In the configuration file/variables:
-    - Set `deployment_type` to "gitlab"
+    - Set `config.git_provider` to "gitlab"
 
   2. In the secrets file/variables:
     - Set your AI model key in the respective section
-    - In the [gitlab] section, set `personal_access_token` (with token from step 1) and `shared_secret` (with secret from step 2)
+    - In the [gitlab] section, set `personal_access_token` (with token from step 2) and `shared_secret` (with secret from step 3)
 
-
-5. Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
+6. Build a Docker image for the app and optionally push it to a Docker repository. We'll use Dockerhub as an example:
 ```
 docker build . -t gitlab_pr_agent --target gitlab_webhook -f docker/Dockerfile
 docker push codiumai/pr-agent:gitlab_webhook  # Push to your Docker repository
 ```
 
-6. Create a webhook in GitLab. Set the URL to ```http[s]://<PR_AGENT_HOSTNAME>/webhook```, the secret token to the generated secret from step 2, and enable the triggers `push`, `comments` and `merge request events`.
+7. Set the environmental variables, the method depends on your docker runtime. Skip this step if you included your secrets/configuration directly in the Docker image.
+
+```
+"CONFIG.GIT_PROVIDER": "gitlab"
+"GITLAB.PERSONAL_ACCESS_TOKEN": "<personal_access_token>"
+"GITLAB.SHARED_SECRET": "<shared_secret>"
+"GITLAB.URL": "https://gitlab.com"
+"OPENAI.KEY": "<your_openai_api_key>"
+```
+
+8. Create a webhook in your GitLab project. Set the URL to ```http[s]://<PR_AGENT_HOSTNAME>/webhook```, the secret token to the generated secret from step 3, and enable the triggers `push`, `comments` and `merge request events`.
+
+9. Test your installation by opening a merge request or commenting on a merge request using one of PR Agent's commands.
 
-7. Test your installation by opening a merge request or commenting on a merge request using one of CodiumAI's commands.
-boxes

docs/docs/installation/index.md

@@ -1,21 +1,17 @@
 # Installation
 
-## Self-hosted Qodo Merge
-If you choose to host your own Qodo Merge, you first need to acquire two tokens:
+## Self-hosted PR-Agent
 
-1. An OpenAI key from [here](https://platform.openai.com/api-keys), with access to GPT-4 (or a key for other [language models](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/), if you prefer).
-2. A GitHub\GitLab\BitBucket personal access token (classic), with the repo scope. [GitHub from [here](https://github.com/settings/tokens)]
-
-There are several ways to use self-hosted Qodo Merge:
+There are several ways to use self-hosted PR-Agent:
 
 - [Locally](./locally.md)
-- [GitHub](./github.md)
-- [GitLab](./gitlab.md)
-- [BitBucket](./bitbucket.md)
-- [Azure DevOps](./azure.md)
+- [GitHub integration](./github.md)
+- [GitLab integration](./gitlab.md)
+- [BitBucket integration](./bitbucket.md)
+- [Azure DevOps integration](./azure.md)
 
-## Qodo Merge Pro 💎
-Qodo Merge Pro, an app hosted by CodiumAI for GitHub\GitLab\BitBucket, is also available.
+## Qodo Merge 💎
+Qodo Merge, an app hosted by QodoAI for GitHub\GitLab\BitBucket, is also available.
 <br>
-With Qodo Merge Pro, installation is as simple as signing up and adding the Qodo Merge app to your relevant repo.
-See [here](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/) for more details.
+With Qodo Merge, installation is as simple as adding the Qodo Merge app to your relevant repositories.
+See [here](https://qodo-merge-docs.qodo.ai/installation/qodo_merge/) for more details.

docs/docs/installation/locally.md

@@ -1,3 +1,77 @@
+To run PR-Agent locally, you first need to acquire two keys:
+
+1. An OpenAI key from [here](https://platform.openai.com/api-keys){:target="_blank"}, with access to GPT-4 and o3-mini (or a key for other [language models](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/), if you prefer).
+2. A personal access token from your Git platform (GitHub, GitLab, BitBucket) with repo scope. GitHub token, for example, can be issued from [here](https://github.com/settings/tokens){:target="_blank"}
+
+
+## Using Docker image
+
+A list of the relevant tools can be found in the [tools guide](../tools/).
+
+To invoke a tool (for example `review`), you can run PR-Agent directly from the Docker image. Here's how:
+
+- For GitHub:
+    ```
+    docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+    ```
+    If you are using GitHub enterprise server, you need to specify the custom url as variable.
+    For example, if your GitHub server is at `https://github.mycompany.com`, add the following to the command:
+    ```
+    -e GITHUB.BASE_URL=https://github.mycompany.com/api/v3
+    ```
+
+- For GitLab:
+    ```
+    docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
+    ```
+
+    If you have a dedicated GitLab instance, you need to specify the custom url as variable:
+    ```
+    -e GITLAB.URL=<your gitlab instance url>
+    ```
+
+- For BitBucket:
+    ```
+    docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
+    ```
+
+For other git providers, update `CONFIG.GIT_PROVIDER` accordingly and check the [`pr_agent/settings/.secrets_template.toml`](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/.secrets_template.toml) file for environment variables expected names and values.
+
+### Utilizing environment variables
+
+It is also possible to provide or override the configuration by setting the corresponding environment variables.
+You can define the corresponding environment variables by following this convention: `<TABLE>__<KEY>=<VALUE>` or `<TABLE>.<KEY>=<VALUE>`.
+The `<TABLE>` refers to a table/section in a configuration file and `<KEY>=<VALUE>` refers to the key/value pair of a setting in the configuration file.
+
+For example, suppose you want to run `pr_agent` that connects to a self-hosted GitLab instance similar to an example above.
+You can define the environment variables in a plain text file named `.env` with the following content:
+
+```
+CONFIG__GIT_PROVIDER="gitlab"
+GITLAB__URL="<your url>"
+GITLAB__PERSONAL_ACCESS_TOKEN="<your token>"
+OPENAI__KEY="<your key>"
+```
+
+Then, you can run `pr_agent` using Docker with the following command:
+
+```shell
+docker run --rm -it --env-file .env codiumai/pr-agent:latest <tool> <tool parameter>
+```
+
+---
+
+### I get an error when running the Docker image. What should I do?
+
+If you encounter an error when running the Docker image, it is almost always due to a misconfiguration of api keys or tokens.
+
+Note that litellm, which is used by pr-agent, sometimes returns non-informative error messages such as `APIError: OpenAIException - Connection error.`
+Carefully check the api keys and tokens you provided and make sure they are correct.
+Adjustments may be needed depending on your llm provider.
+
+For example, for Azure OpenAI, additional keys are [needed](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/#azure).
+Same goes for other providers, make sure to check the [documentation](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/#changing-a-model)
+
 ## Using pip package
 
 Install the package:
@@ -35,40 +109,6 @@ if __name__ == '__main__':
     main()
 ```
 
-## Using Docker image
-
-A list of the relevant tools can be found in the [tools guide](../tools/ask.md).
-
-To invoke a tool (for example `review`), you can run directly from the Docker image. Here's how:
-
-- For GitHub:
-    ```
-    docker run --rm -it -e OPENAI.KEY=<your key> -e GITHUB.USER_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
-    ```
-    If you are using GitHub enterprise server, you need to specify the custom url as variable.
-    For example, if your GitHub server is at `https://github.mycompany.com`, add the following to the command:
-    ```
-    -e GITHUB.BASE_URL=https://github.mycompany.com/api/v3
-    ```
-
-- For GitLab:
-    ```
-    docker run --rm -it -e OPENAI.KEY=<your key> -e CONFIG.GIT_PROVIDER=gitlab -e GITLAB.PERSONAL_ACCESS_TOKEN=<your token> codiumai/pr-agent:latest --pr_url <pr_url> review
-    ```
-
-    If you have a dedicated GitLab instance, you need to specify the custom url as variable:
-    ```
-    -e GITLAB.URL=<your gitlab instance url>
-    ```
-
-- For BitBucket:
-    ```
-    docker run --rm -it -e CONFIG.GIT_PROVIDER=bitbucket -e OPENAI.KEY=$OPENAI_API_KEY -e BITBUCKET.BEARER_TOKEN=$BITBUCKET_BEARER_TOKEN codiumai/pr-agent:latest --pr_url=<pr_url> review
-    ```
-
-For other git providers, update CONFIG.GIT_PROVIDER accordingly, and check the `pr_agent/settings/.secrets_template.toml` file for the environment variables expected names and values.
-
----
 
 ## Run from source
 

docs/docs/installation/pr_agent.md

@@ -0,0 +1,49 @@
+# PR-Agent Installation Guide
+
+PR-Agent can be deployed in various environments and platforms. Choose the installation method that best suits your needs:
+
+## 🖥️ Local Installation
+
+Learn how to run PR-Agent locally using:
+
+- Docker image
+- pip package
+- CLI from source code
+
+[View Local Installation Guide →](https://qodo-merge-docs.qodo.ai/installation/locally/)
+
+## 🐙 GitHub Integration
+
+Set up PR-Agent with GitHub as:
+
+- GitHub Action
+- Local GitHub App
+
+[View GitHub Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/github/)
+
+## 🦊 GitLab Integration
+
+Deploy PR-Agent on GitLab as:
+
+- GitLab pipeline job
+- Local GitLab webhook server
+
+[View GitLab Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/gitlab/)
+
+## 🟦 BitBucket Integration
+
+Implement PR-Agent in BitBucket as:
+
+- BitBucket pipeline job
+- Local BitBucket server
+
+[View BitBucket Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/bitbucket/)
+
+## 🔷  Azure DevOps Integration
+
+Configure PR-Agent with Azure DevOps as:
+
+- Azure DevOps pipeline job
+- Local Azure DevOps webhook
+
+[View Azure DevOps Integration Guide →](https://qodo-merge-docs.qodo.ai/installation/azure/)

docs/docs/installation/qodo_merge.md

@@ -1,42 +1,44 @@
-Qodo Merge Pro is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by QodoAI.
-See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for more details about the benefits of using Qodo Merge Pro.
+Qodo Merge is a versatile application compatible with GitHub, GitLab, and BitBucket, hosted by QodoAI.
+See [here](https://qodo-merge-docs.qodo.ai/overview/pr_agent_pro/) for more details about the benefits of using Qodo Merge.
 
-A complimentary two-week trial is provided to all new users. Following the trial period, user licenses (seats) are required for continued access.
+A complimentary two-week trial is provided to all new users (with three additional grace usages). Following the trial period, user licenses (seats) are required for continued access.
 To purchase user licenses, please visit our [pricing page](https://www.qodo.ai/pricing/).
 Once subscribed, users can seamlessly deploy the application across any of their code repositories.
 
-## Install Qodo Merge Pro for GitHub
+## Install Qodo Merge for GitHub
 
 ### GitHub Cloud
 
-Qodo Merge Pro for GitHub cloud is available for installation through the [GitHub Marketplace](https://github.com/apps/qodo-merge-pro).
+Qodo Merge for GitHub cloud is available for installation through the [GitHub Marketplace](https://github.com/apps/qodo-merge-pro).
 
-![Qodo Merge Pro](https://codium.ai/images/pr_agent/pr_agent_pro_install.png){width=468}
+![Qodo Merge](https://codium.ai/images/pr_agent/pr_agent_pro_install.png){width=468}
 
 ### GitHub Enterprise Server
 
-To use Qodo Merge Pro application on your private GitHub Enterprise Server, you will need to contact us for starting an [Enterprise](https://www.codium.ai/pricing/) trial.
+To use Qodo Merge application on your private GitHub Enterprise Server, you will need to [contact](https://www.qodo.ai/contact/#pricing) Qodo for starting an Enterprise trial.
 
 ### GitHub Open Source Projects
 
-For open-source projects, Qodo Merge Pro is available for free usage. To install Qodo Merge Pro for your open-source repositories, use the following marketplace [link](https://github.com/apps/qodo-merge-pro-for-open-source).
+For open-source projects, Qodo Merge is available for free usage. To install Qodo Merge for your open-source repositories, use the following marketplace [link](https://github.com/apps/qodo-merge-pro-for-open-source).
 
-## Install Qodo Merge Pro for Bitbucket
+## Install Qodo Merge for Bitbucket
 
 ###  Bitbucket Cloud
 
-Qodo Merge Pro for Bitbucket Cloud is available for installation through the following [link](https://bitbucket.org/site/addons/authorize?addon_key=d6df813252c37258)
+Qodo Merge for Bitbucket Cloud is available for installation through the following [link](https://bitbucket.org/site/addons/authorize?addon_key=d6df813252c37258)
 
-![Qodo Merge Pro](https://qodo.ai/images/pr_agent/pr_agent_pro_bitbucket_install.png){width=468}
+![Qodo Merge](https://qodo.ai/images/pr_agent/pr_agent_pro_bitbucket_install.png){width=468}
 
 ### Bitbucket Server
 
-To use Qodo Merge Pro application on your private Bitbucket Server, you will need to contact us for starting an [Enterprise](https://www.codium.ai/pricing/) trial.
+To use Qodo Merge application on your private Bitbucket Server, you will need to contact us for starting an [Enterprise](https://www.qodo.ai/pricing/) trial.
 
 
-## Install Qodo Merge Pro for GitLab (Teams & Enterprise)
+## Install Qodo Merge for GitLab 
 
-Since GitLab platform does not support apps, installing Qodo Merge Pro for GitLab is a bit more involved, and requires the following steps:
+### GitLab Cloud
+
+Since GitLab platform does not support apps, installing Qodo Merge for GitLab is a bit more involved, and requires the following steps:
 
 #### Step 1
 
@@ -79,3 +81,7 @@ Enable SSL verification: Check the box.
 You’re all set!
 
 Open a new merge request or add a MR comment with one of Qodo Merge’s commands such as /review, /describe or /improve.
+
+### GitLab Server
+
+For a trial period of two weeks on your private GitLab Server, the same [installation steps](#gitlab-cloud) as for GitLab Cloud apply. After the trial period, you will need to [contact](https://www.qodo.ai/contact/#pricing) Qodo for moving to an Enterprise account.

docs/docs/overview/data_privacy.md

@@ -1,12 +1,12 @@
-## Self-hosted Qodo Merge
+## Self-hosted PR-Agent
 
-- If you self-host Qodo Merge with your OpenAI (or other LLM provider) API key, it is between you and the provider. We don't send your code data to Qodo Merge servers.
+- If you self-host PR-Agent with your OpenAI (or other LLM provider) API key, it is between you and the provider. We don't send your code data to Qodo servers.
 
-## Qodo Merge Pro 💎
+## Qodo Merge 💎
 
-- When using Qodo Merge Pro 💎, hosted by CodiumAI, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
+- When using Qodo Merge💎, hosted by Qodo, we will not store any of your data, nor will we use it for training. You will also benefit from an OpenAI account with zero data retention.
 
-- For certain clients, CodiumAI-hosted Qodo Merge Pro will use CodiumAI’s proprietary models. If this is the case, you will be notified.
+- For certain clients, Qodo Merge will use Qodo’s proprietary models. If this is the case, you will be notified.
 
 - No passive collection of Code and Pull Requests’ data — Qodo Merge will be active only when you invoke it, and it will then extract and analyze only data relevant to the executed command and queried pull request.
 

docs/docs/overview/index.md

@@ -1,93 +0,0 @@
-# Overview
-
-Qodo Merge is an open-source tool to help efficiently review and handle pull requests.
-
-- See the [Installation Guide](./installation/index.md) for instructions on installing and running the tool on different git platforms.
-
-- See the [Usage Guide](./usage-guide/index.md) for instructions on running the Qodo Merge commands via different interfaces, including _CLI_, _online usage_, or by _automatically triggering_ them when a new PR is opened.
-
-- See the [Tools Guide](./tools/index.md) for a detailed description of the different tools.
-
-
-## Qodo Merge Docs Smart Search
-
-To search the documentation site using natural language:
-
-1) Comment `/help "your question"` in either:
-
-   - A pull request where Qodo Merge is installed
-   - A [PR Chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat)
-
-2) Qodo Merge will respond with an [answer](https://github.com/Codium-ai/pr-agent/pull/1241#issuecomment-2365259334) that includes relevant documentation links.
-
-
-## Qodo Merge Features
-
-Qodo Merge offers extensive pull request functionalities across various git providers.
-
-|       |                                                                                                                       | GitHub | Gitlab | Bitbucket | Azure DevOps |
-|-------|-----------------------------------------------------------------------------------------------------------------------|:------:|:------:|:---------:|:------------:|
-| TOOLS | Review                                                                                                                |   ✅    |   ✅    |   ✅       |      ✅      |
-|       | ⮑ Incremental                                                                                                         |   ✅    |        |            |              |
-|       | Ask                                                                                                                   |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Describe                                                                                                              |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | ⮑ [Inline file summary](https://qodo-merge-docs.qodo.ai/tools/describe/#inline-file-summary){:target="_blank"} 💎     |   ✅    |   ✅    |           |      ✅      |
-|       | Improve                                                                                                               |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | ⮑ Extended                                                                                                            |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | [Custom Prompt](./tools/custom_prompt.md){:target="_blank"} 💎                                                        |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Reflect and Review                                                                                                    |   ✅    |   ✅    |   ✅        |      ✅      |
-|       | Update CHANGELOG.md                                                                                                   |   ✅    |   ✅    |   ✅        |      ️       |
-|       | Find Similar Issue                                                                                                    |   ✅    |        |             |      ️       |
-|       | [Add PR Documentation](./tools/documentation.md){:target="_blank"} 💎                                                 |   ✅    |   ✅    |          |      ✅      |
-|       | [Generate Custom Labels](./tools/describe.md#handle-custom-labels-from-the-repos-labels-page-💎){:target="_blank"} 💎 |   ✅    |   ✅    |            |      ✅      |
-|       | [Analyze PR Components](./tools/analyze.md){:target="_blank"} 💎                                                      |   ✅    |   ✅    |       |      ✅      |
-|       |                                                                                                                       |        |        |            |      ️       |
-| USAGE | CLI                                                                                                                   |   ✅    |   ✅    |   ✅       |      ✅      |
-|       | App / webhook                                                                                                         |   ✅    |   ✅    |    ✅        |      ✅      |
-|       | Actions                                                                                                               |   ✅    |        |            |      ️       |
-|       |                                                                                                                       |        |        |            |
-| CORE  | PR compression                                                                                                        |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Repo language prioritization                                                                                          |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Adaptive and token-aware file patch fitting                                                                           |   ✅    |   ✅    |   ✅     |   ✅        |
-|       | Multiple models support                                                                                               |   ✅    |   ✅    |   ✅       |   ✅        |
-|       | Incremental PR review                                                                                                 |   ✅    |        |            |           |
-|       | [Static code analysis](./tools/analyze.md/){:target="_blank"} 💎                                                      |   ✅    |   ✅     |    ✅    |   ✅        |
-|       | [Multiple configuration options](./usage-guide/configuration_options.md){:target="_blank"} 💎                         |   ✅    |   ✅     |    ✅    |   ✅        |
-
-💎 marks a feature available only in [Qodo Merge Pro](https://www.codium.ai/pricing/){:target="_blank"}
-
-
-## Example Results
-<hr>
-
-#### [/describe](https://github.com/Codium-ai/pr-agent/pull/530)
-<figure markdown="1">
-![/describe](https://www.codium.ai/images/pr_agent/describe_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/review](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099151)
-<figure markdown="1">
-![/review](https://www.codium.ai/images/pr_agent/review_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/improve](https://github.com/Codium-ai/pr-agent/pull/732#issuecomment-1975099159)
-<figure markdown="1">
-![/improve](https://www.codium.ai/images/pr_agent/improve_new_short_main.png){width=512}
-</figure>
-<hr>
-
-#### [/generate_labels](https://github.com/Codium-ai/pr-agent/pull/530)
-<figure markdown="1">
-![/generate_labels](https://www.codium.ai/images/pr_agent/geneare_custom_labels_main_short.png){width=300}
-</figure>
-<hr>
-
-## How it Works
-
-The following diagram illustrates Qodo Merge tools and their flow:
-
-![Qodo Merge Tools](https://codium.ai/images/pr_agent/diagram-v0.9.png)
-
-Check out the [PR Compression strategy](core-abilities/index.md) page for more details on how we convert a code diff to a manageable LLM prompt

docs/docs/overview/pr_agent_pro.md

@@ -1,51 +1,52 @@
 ### Overview
 
-[Qodo Merge Pro](https://www.codium.ai/pricing/) is a hosted version of open-source [Qodo Merge (PR-Agent)](https://github.com/Codium-ai/pr-agent). A complimentary two-week trial is offered, followed by a monthly subscription fee.
-Qodo Merge Pro is designed for companies and teams that require additional features and capabilities. It provides the following benefits:
+[Qodo Merge](https://www.codium.ai/pricing/){:target="_blank"} is a paid, hosted version of open-source [PR-Agent](https://github.com/Codium-ai/pr-agent){:target="_blank"}. A complimentary two-week trial is offered, followed by a monthly subscription fee.
+Qodo Merge is designed for companies and teams that require additional features and capabilities. It provides the following benefits:
 
 1. **Fully managed** - We take care of everything for you - hosting, models, regular updates, and more. Installation is as simple as signing up and adding the Qodo Merge app to your GitHub\GitLab\BitBucket repo.
 
-2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge Pro will employ zero data retention, and will use an OpenAI and Claude accounts with zero data retention.
+2. **Improved privacy** - No data will be stored or used to train models. Qodo Merge will employ zero data retention, and will use an OpenAI and Claude accounts with zero data retention.
 
-3. **Improved support** - Qodo Merge Pro users will receive priority support, and will be able to request new features and capabilities.
+3. **Improved support** - Qodo Merge users will receive priority support, and will be able to request new features and capabilities.
 
-4. **Supporting self-hosted git servers** - Qodo Merge Pro can be installed on GitHub Enterprise Server, GitLab, and BitBucket. For more information, see the [installation guide](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/).
+4. **Supporting self-hosted git servers** - Qodo Merge can be installed on GitHub Enterprise Server, GitLab, and BitBucket. For more information, see the [installation guide](https://qodo-merge-docs.qodo.ai/installation/pr_agent_pro/).
 
-5. **PR Chat** - Qodo Merge Pro allows you to engage in [private chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) about your pull requests on private repositories.
+5. **PR Chat** - Qodo Merge allows you to engage in [private chat](https://qodo-merge-docs.qodo.ai/chrome-extension/features/#pr-chat) about your pull requests on private repositories.
 
 ### Additional features
 
-Here are some of the additional features and capabilities that Qodo Merge Pro offers:
+Here are some of the additional features and capabilities that Qodo Merge offers:
 
 | Feature                                                                                                              | Description                                                                                                                                                      |
 |----------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| [**Model selection**](https://qodo-merge-docs.qodo.ai/usage-guide/PR_agent_pro_models/)          | Choose the model that best fits your needs, among top models like `GPT4` and `Claude-Sonnet-3.5`
+| [**Model selection**](https://qodo-merge-docs.qodo.ai/usage-guide/PR_agent_pro_models/)          | Choose the model that best fits your needs, among top models like `Claude Sonnet` and `o3-mini`
 | [**Global and wiki configuration**](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/)              | Control configurations for many repositories from a single location; <br>Edit configuration of a single repo without committing code                              |
 | [**Apply suggestions**](https://qodo-merge-docs.qodo.ai/tools/improve/#overview)                                     | Generate committable code from the relevant suggestions interactively by clicking on a checkbox                                                                   |
 | [**Suggestions impact**](https://qodo-merge-docs.qodo.ai/tools/improve/#assessing-impact)                         | Automatically mark suggestions that were implemented by the user (either directly in GitHub, or indirectly in the IDE) to enable tracking of the impact of the suggestions |
 | [**CI feedback**](https://qodo-merge-docs.qodo.ai/tools/ci_feedback/) | Automatically analyze failed CI checks on GitHub and provide actionable feedback in the PR conversation, helping to resolve issues quickly |
-| [**Advanced usage statistics**](https://www.codium.ai/contact/#/)                                                    | Qodo Merge Pro offers detailed statistics at user, repository, and company levels, including metrics about Qodo Merge usage, and also general statistics and insights |
+| [**Advanced usage statistics**](https://www.codium.ai/contact/#/)                                                    | Qodo Merge offers detailed statistics at user, repository, and company levels, including metrics about Qodo Merge usage, and also general statistics and insights |
 | [**Incorporating companies' best practices**](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices)         | Use the companies' best practices as reference to increase the effectiveness and the relevance of the code suggestions                                           |
 | [**Interactive triggering**](https://qodo-merge-docs.qodo.ai/tools/analyze/#example-usage)                           | Interactively apply different tools via the `analyze` command                                                                                                    |
-| [**Custom labels**](https://qodo-merge-docs.qodo.ai/tools/describe/#handle-custom-labels-from-the-repos-labels-page) | Define custom labels for Qodo Merge to assign to the PR                                                                                                            |
+| [**Custom labels**](https://qodo-merge-docs.qodo.ai/tools/describe/#handle-custom-labels-from-the-repos-labels-page) | Define custom labels for Qodo Merge to assign to the PR                                                                                                           |
 
 ### Additional tools
 
-Here are additional tools that are available only for Qodo Merge Pro users:
+Here are additional tools that are available only for Qodo Merge users:
 
-| Feature | Description |
-|---------|-------------|
+| Feature                                                                               | Description |
+|---------------------------------------------------------------------------------------|-------------|
 | [**Custom Prompt Suggestions**](https://qodo-merge-docs.qodo.ai/tools/custom_prompt/) | Generate code suggestions based on custom prompts from the user |
-| [**Analyze PR components**](https://qodo-merge-docs.qodo.ai/tools/analyze/) | Identify the components that changed in the PR, and enable to interactively apply different tools to them |
-| [**Tests**](https://qodo-merge-docs.qodo.ai/tools/test/) | Generate tests for code components that changed in the PR |
-| [**PR documentation**](https://qodo-merge-docs.qodo.ai/tools/documentation/) | Generate docstring for code components that changed in the PR |
-| [**Improve Component**](https://qodo-merge-docs.qodo.ai/tools/improve_component/) | Generate code suggestions for code components that changed in the PR |
-| [**Similar code search**](https://qodo-merge-docs.qodo.ai/tools/similar_code/) | Search for similar code in the repository, organization, or entire GitHub |
+| [**Analyze PR components**](https://qodo-merge-docs.qodo.ai/tools/analyze/)           | Identify the components that changed in the PR, and enable to interactively apply different tools to them |
+| [**Tests**](https://qodo-merge-docs.qodo.ai/tools/test/)                              | Generate tests for code components that changed in the PR |
+| [**PR documentation**](https://qodo-merge-docs.qodo.ai/tools/documentation/)          | Generate docstring for code components that changed in the PR |
+| [**Improve Component**](https://qodo-merge-docs.qodo.ai/tools/improve_component/)     | Generate code suggestions for code components that changed in the PR |
+| [**Similar code search**](https://qodo-merge-docs.qodo.ai/tools/similar_code/)        | Search for similar code in the repository, organization, or entire GitHub |
+| [**Code implementation**](https://qodo-merge-docs.qodo.ai/tools/implement/)        | Generates implementation code from review suggestions |
 
 
 ### Supported languages
 
-Qodo Merge Pro leverages the world's leading code models - Claude 3.5 Sonnet and GPT-4.
+Qodo Merge leverages the world's leading code models, such as Claude 3.7 Sonnet and o3-mini.
 As a result, its primary tools such as `describe`, `review`, and `improve`, as well as the PR-chat feature, support virtually all programming languages.
 
-For specialized commands that require static code analysis, Qodo Merge Pro offers support for specific languages. For more details about features that require static code analysis, please refer to the [documentation](https://qodo-merge-docs.qodo.ai/tools/analyze/#overview).
+For specialized commands that require static code analysis, Qodo Merge offers support for specific languages. For more details about features that require static code analysis, please refer to the [documentation](https://qodo-merge-docs.qodo.ai/tools/analyze/#overview).

docs/docs/tools/analyze.md

@@ -14,6 +14,5 @@ An example result:
 
 ![Analyze 1](https://codium.ai/images/pr_agent/analyze_1.png){width=750}
 
-**Notes**
-
-- Language that are currently supported: Python, Java, C++, JavaScript, TypeScript, C#.
+!!! note "Language that are currently supported:"
+    Python, Java, C++, JavaScript, TypeScript, C#.

docs/docs/tools/ask.md

@@ -38,20 +38,20 @@ where `https://real_link_to_image` is the direct link to the image.
 Note that GitHub has a built-in mechanism of pasting images in comments. However, pasted image does not provide a direct link.
 To get a direct link to an image, we recommend using the following scheme:
 
-1) First, post a comment that contains **only** the image:
+1\. First, post a comment that contains **only** the image:
 
 ![Ask image1](https://codium.ai/images/pr_agent/ask_images1.png){width=512}
 
-2) Quote reply to that comment:
+2\. Quote reply to that comment:
 
 ![Ask image2](https://codium.ai/images/pr_agent/ask_images2.png){width=512}
 
-3) In the screen opened, type the question below the image:
+3\. In the screen opened, type the question below the image:
 
 ![Ask image3](https://codium.ai/images/pr_agent/ask_images3.png){width=512}
 ![Ask image4](https://codium.ai/images/pr_agent/ask_images4.png){width=512}
 
-4) Post the comment, and receive the answer:
+4\. Post the comment, and receive the answer:
 
 ![Ask image5](https://codium.ai/images/pr_agent/ask_images5.png){width=512}
 

docs/docs/tools/custom_labels.md

@@ -28,7 +28,7 @@ When working from CLI, you need to apply the [configuration changes](#configurat
 To enable custom labels, you need to apply the [configuration changes](#configuration-options) to the local `.pr_agent.toml` file in your repository.
 
 #### 3. Handle custom labels from the Repo's labels page 💎
-> This feature is available only in Qodo Merge Pro
+> This feature is available only in Qodo Merge
 
 * GitHub : `https://github.com/{owner}/{repo}/labels`, or click on the "Labels" tab in the issues or PRs page.
 * GitLab : `https://gitlab.com/{owner}/{repo}/-/labels`, or click on "Manage" -> "Labels" on the left menu.

docs/docs/tools/custom_prompt.md

@@ -51,8 +51,8 @@ Results obtained with the prompt above:
 
 ## Configuration options
 
-`prompt`: the prompt for the tool. It should be a multi-line string.
+- `prompt`: the prompt for the tool. It should be a multi-line string.
 
-`num_code_suggestions`: number of code suggestions provided by the 'custom_prompt' tool. Default is 4.
+- `num_code_suggestions_per_chunk`: number of code suggestions provided by the 'custom_prompt' tool, per chunk. Default is 3.
 
-`enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.
+- `enable_help_text`: if set to true, the tool will display a help text in the comment. Default is true.

docs/docs/tools/describe.md

@@ -46,56 +46,56 @@ publish_labels = true
 
 !!! example "Possible configurations"
 
-<table>
-  <tr>
-    <td><b>publish_labels</b></td>
-    <td>If set to true, the tool will publish labels to the PR. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>publish_description_as_comment</b></td>
-    <td>If set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the original description. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>publish_description_as_comment_persistent</b></td>
-    <td>If set to true and `publish_description_as_comment` is true, the tool will publish the description as a persistent comment to the PR. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>add_original_user_description</b></td>
-    <td>If set to true, the tool will add the original user description to the generated description. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>generate_ai_title</b></td>
-    <td>If set to true, the tool will also generate an AI title for the PR. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>extra_instructions</b></td>
-    <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ..."</td>
-  </tr>
-  <tr>
-    <td><b>enable_pr_type</b></td>
-    <td>If set to false, it will not show the `PR type` as a text value in the description content. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>final_update_message</b></td>
-    <td>If set to true, it will add a comment message [`PR Description updated to latest commit...`](https://github.com/Codium-ai/pr-agent/pull/499#issuecomment-1837412176) after finishing calling `/describe`. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>enable_semantic_files_types</b></td>
-    <td>If set to true, "Changes walkthrough" section will be generated. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>collapsible_file_list</b></td>
-    <td>If set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if there are more than 8 files. Default is "adaptive".</td>
-  </tr>
-  <tr>
-    <td><b>enable_large_pr_handling</b></td>
-    <td>Pro feature. If set to true, in case of a large PR the tool will make several calls to the AI and combine them to be able to cover more files. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>enable_help_text</b></td>
-    <td>If set to true, the tool will display a help text in the comment. Default is false.</td>
-  </tr>
-</table>
+    <table>
+      <tr>
+        <td><b>publish_labels</b></td>
+        <td>If set to true, the tool will publish labels to the PR. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>publish_description_as_comment</b></td>
+        <td>If set to true, the tool will publish the description as a comment to the PR. If false, it will overwrite the original description. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>publish_description_as_comment_persistent</b></td>
+        <td>If set to true and `publish_description_as_comment` is true, the tool will publish the description as a persistent comment to the PR. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>add_original_user_description</b></td>
+        <td>If set to true, the tool will add the original user description to the generated description. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>generate_ai_title</b></td>
+        <td>If set to true, the tool will also generate an AI title for the PR. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>extra_instructions</b></td>
+        <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ..."</td>
+      </tr>
+      <tr>
+        <td><b>enable_pr_type</b></td>
+        <td>If set to false, it will not show the `PR type` as a text value in the description content. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>final_update_message</b></td>
+        <td>If set to true, it will add a comment message [`PR Description updated to latest commit...`](https://github.com/Codium-ai/pr-agent/pull/499#issuecomment-1837412176) after finishing calling `/describe`. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>enable_semantic_files_types</b></td>
+        <td>If set to true, "Changes walkthrough" section will be generated. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>collapsible_file_list</b></td>
+        <td>If set to true, the file list in the "Changes walkthrough" section will be collapsible. If set to "adaptive", the file list will be collapsible only if there are more than 8 files. Default is "adaptive".</td>
+      </tr>
+      <tr>
+        <td><b>enable_large_pr_handling</b></td>
+        <td>Pro feature. If set to true, in case of a large PR the tool will make several calls to the AI and combine them to be able to cover more files. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>enable_help_text</b></td>
+        <td>If set to true, the tool will display a help text in the comment. Default is false.</td>
+      </tr>
+    </table>
 
 
 ## Inline file summary 💎
@@ -143,7 +143,7 @@ The marker `pr_agent:type` will be replaced with the PR type, `pr_agent:summary`
 
 ![Describe markers before](https://codium.ai/images/pr_agent/describe_markers_before.png){width=512}
 
-&rarr;
+becomes
 
 ![Describe markers after](https://codium.ai/images/pr_agent/describe_markers_after.png){width=512}
 

docs/docs/tools/documentation.md

@@ -27,7 +27,6 @@ You can state a name of a specific component in the PR to get documentation only
  - `docs_style`: The exact style of the documentation (for python docstring). you can choose between: `google`, `numpy`, `sphinx`, `restructuredtext`, `plain`. Default is `sphinx`.
  - `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".
 
-**Notes**
-
-- Language that are currently fully supported: Python, Java, C++, JavaScript, TypeScript, C#.
-- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
+!!! note "Notes"
+    - The following languages are currently supported: Python, Java, C++, JavaScript, TypeScript, C#.
+    - This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.

docs/docs/tools/help.md

@@ -1,6 +1,6 @@
 ## Overview
 The `help` tool provides a list of all the available tools and their descriptions.
-For Qodo Merge Pro users, it also enables to trigger each tool by checking the relevant box.
+For Qodo Merge users, it also enables to trigger each tool by checking the relevant box.
 
 It can be invoked manually by commenting on any PR:
 ```

docs/docs/tools/help_docs.md

@@ -0,0 +1,108 @@
+## Overview
+
+The `help_docs` tool can answer a free-text question based on a git documentation folder.
+
+It can be invoked manually by commenting on any PR or Issue:
+```
+/help_docs "..."
+```
+Or configured to be triggered automatically when a [new issue is opened](#run-as-a-github-action).
+
+The tool assumes by default that the documentation is located in the root of the repository, at `/docs` folder.
+However, this can be customized by setting the `docs_path` configuration option:
+
+```toml
+[pr_help_docs]
+repo_url = ""                 # The repository to use as context
+docs_path = "docs"            # The documentation folder
+repo_default_branch = "main"  # The branch to use in case repo_url overwritten
+
+```
+
+See more configuration options in the [Configuration options](#configuration-options) section.
+
+## Example usage
+
+[//]: # (#### Asking a question about this repository:)
+
+[//]: # (![help_docs on the documentation of this repository](https://codium.ai/images/pr_agent/help_docs_comment.png){width=512})
+
+**Asking a question about another repository**
+
+![help_docs on the documentation of another repository](https://codium.ai/images/pr_agent/help_docs_comment_explicit_git.png){width=512}
+
+**Response**:
+
+![help_docs response](https://codium.ai/images/pr_agent/help_docs_response.png){width=512}
+
+## Run automatically when a new issue is opened
+
+You can configure PR-Agent to run `help_docs` automatically on any newly created issue.
+This can be useful, for example, for providing immediate feedback to users who open issues with questions on open-source projects with extensive documentation.
+
+Here's how:
+
+1) Follow the steps depicted under [Run as a Github Action](https://qodo-merge-docs.qodo.ai/installation/github/#run-as-a-github-action) to create a new workflow, such as:`.github/workflows/help_docs.yml`:
+
+2) Edit your yaml file to the following:
+
+```yaml
+name: Run pr agent on every opened issue, respond to user comments on an issue
+
+#When the action is triggered
+on:
+  issues:
+    types: [opened] #New issue
+
+# Read env. variables
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  GITHUB_API_URL: ${{ github.api_url }}
+  GIT_REPO_URL: ${{ github.event.repository.clone_url }}
+  ISSUE_URL: ${{ github.event.issue.html_url || github.event.comment.html_url }}
+  ISSUE_BODY: ${{ github.event.issue.body || github.event.comment.body }}
+  OPENAI_KEY: ${{ secrets.OPENAI_KEY }}
+
+# The actual set of actions
+jobs:
+  issue_agent:
+    runs-on: ubuntu-latest
+    if: ${{ github.event.sender.type != 'Bot' }} #Do not respond to bots
+
+    # Set required permissions
+    permissions:
+      contents: read    # For reading repository contents
+      issues: write     # For commenting on issues
+
+    steps:
+      - name: Run PR Agent on Issues
+        if: ${{ env.ISSUE_URL != '' }}
+        uses: docker://codiumai/pr-agent:latest
+        with:
+          entrypoint: /bin/bash #Replace invoking cli.py directly with a shell
+          args: |
+            -c "cd /app && \
+            echo 'Running Issue Agent action step on ISSUE_URL=$ISSUE_URL' && \
+            export config__git_provider='github' && \
+            export github__user_token=$GITHUB_TOKEN && \            
+            export github__base_url=$GITHUB_API_URL && \
+            export openai__key=$OPENAI_KEY && \
+            python -m pr_agent.cli --issue_url=$ISSUE_URL --pr_help_docs.repo_url="..." --pr_help_docs.docs_path="..." --pr_help_docs.openai_key=$OPENAI_KEY && \help_docs \"$ISSUE_BODY\""
+```
+
+3) Following completion of the remaining steps (such as adding secrets and relevant configurations, such as `repo_url` and `docs_path`) merge this change to your main branch.
+When a new issue is opened, you should see a comment from `github-actions` bot with an auto response, assuming the question is related to the documentation of the repository.
+---
+
+
+## Configuration options
+
+Under the section `pr_help_docs`, the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L50) contains options to customize the 'help docs' tool:
+
+- `repo_url`: If not overwritten, will use the repo from where the context came from (issue or PR), otherwise - use the given repo as context.
+- `repo_default_branch`: The branch to use in case repo_url overwritten, otherwise - has no effect.
+- `docs_path`: Relative path from root of repository (either the one this PR has been issued for, or above repo url).
+- `exclude_root_readme`:  Whether or not to exclude the root README file for querying the model.
+- `supported_doc_exts` : Which file extensions should be included for the purpose of querying the model.
+
+---

docs/docs/tools/implement.md

@@ -0,0 +1,54 @@
+`Platforms supported: GitHub, GitLab, Bitbucket`
+
+## Overview
+
+The `implement` tool converts human code review discussions and feedback into ready-to-commit code changes.
+It leverages LLM technology to transform PR comments and review suggestions into concrete implementation code, helping developers quickly turn feedback into working solutions.
+
+## Usage Scenarios
+
+
+### For Reviewers
+
+Reviewers can request code changes by:
+
+1. Selecting the code block to be modified.
+2. Adding a comment with the syntax: 
+```
+/implement <code-change-description>
+```
+
+![implement1](https://codium.ai/images/pr_agent/implement1.png){width=640}
+
+
+### For PR Authors
+
+PR authors can implement suggested changes by replying to a review comment using either: <br>
+1. Add specific implementation details as described above
+```
+/implement <code-change-description>
+```
+2. Use the original review comment as instructions
+```
+/implement
+```
+
+![implement2](https://codium.ai/images/pr_agent/implement2.png){width=640}
+
+### For Referencing Comments
+
+You can reference and implement changes from any comment by:
+```
+/implement <link-to-review-comment>
+```
+
+![implement3](https://codium.ai/images/pr_agent/implement3.png){width=640}
+
+Note that the implementation will occur within the review discussion thread.
+
+
+**Configuration options**
+
+- Use `/implement` to implement code change within and based on the review discussion.
+- Use `/implement <code-change-description>` inside a review discussion to implement specific instructions.
+- Use `/implement <link-to-review-comment>` to indirectly call the tool from any comment.

docs/docs/tools/improve.md

@@ -9,8 +9,9 @@ The tool can be triggered automatically every time a new PR is [opened](../usage
 
 ![code_suggestions_as_comment_open.png](https://codium.ai/images/pr_agent/code_suggestions_as_comment_open.png){width=512}
 
-Note that the `Apply this suggestion` checkbox, which interactively converts a suggestion into a commitable code comment, is available only for Qodo Merge Pro 💎 users.
-
+!!! note "The following features are available only for Qodo Merge 💎 users:"
+    - The `Apply this suggestion` checkbox, which interactively converts a suggestion into a committable code comment
+    - The `More` checkbox to generate additional suggestions
 
 ## Example usage
 
@@ -52,9 +53,10 @@ num_code_suggestions_per_chunk = ...
 - The `pr_commands` lists commands that will be executed automatically when a PR is opened.
 - The `[pr_code_suggestions]` section contains the configurations for the `improve` tool you want to edit (if any)
 
-### Assessing Impact 💎
+### Assessing Impact
+>`💎 feature`
 
-Note that Qodo Merge pro tracks two types of implementations:
+Qodo Merge tracks two types of implementations for tracking implemented suggestions:
 
 - Direct implementation - when the user directly applies the suggestion by clicking the `Apply` checkbox.
 - Indirect implementation - when the user implements the suggestion in their IDE environment. In this case, Qodo Merge will utilize, after each commit, a dedicated logic to identify if a suggestion was implemented, and will mark it as implemented.
@@ -67,10 +69,10 @@ In post-process, Qodo Merge counts the number of suggestions that were implement
 
 ![code_suggestions_asses_impact_stats_2](https://codium.ai/images/pr_agent/code_suggestions_asses_impact_stats_2.png){width=512}
 
-## Suggestion tracking 💎
-`Platforms supported: GitHub, GitLab`
+## Suggestion tracking
+>`💎 feature. Platforms supported: GitHub, GitLab`
 
-Qodo Merge employs an novel detection system to automatically [identify](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) AI code suggestions that PR authors have accepted and implemented.
+Qodo Merge employs a novel detection system to automatically [identify](https://qodo-merge-docs.qodo.ai/core-abilities/impact_evaluation/) AI code suggestions that PR authors have accepted and implemented.
 
 Accepted suggestions are also automatically documented in a dedicated wiki page called `.pr_agent_accepted_suggestions`, allowing users to track historical changes, assess the tool's effectiveness, and learn from previously implemented recommendations in the repository.
 An example [result](https://github.com/Codium-ai/pr-agent/wiki/.pr_agent_accepted_suggestions):
@@ -101,8 +103,6 @@ The `improve` tool can be further customized by providing additional instruction
 
 ### Extra instructions
 
->`Platforms supported: GitHub, GitLab, Bitbucket, Azure DevOps`
-
 You can use the `extra_instructions` configuration option to give the AI model additional instructions for the `improve` tool.
 Be specific, clear, and concise in the instructions. With extra instructions, you are the prompter.
 
@@ -118,14 +118,14 @@ extra_instructions="""\
 ```
 Use triple quotes to write multi-line instructions. Use bullet points or numbers to make the instructions more readable.
 
-### Best practices 💎
+### Best practices
 
->`Platforms supported: GitHub, GitLab, Bitbucket`
+> `💎 feature. Platforms supported: GitHub, GitLab, Bitbucket`
 
-Another option to give additional guidance to the AI model is by creating a dedicated [**wiki page**](https://github.com/Codium-ai/pr-agent/wiki) called `best_practices.md`.
+Another option to give additional guidance to the AI model is by creating a `best_practices.md` file in your repository's root directory.
 This page can contain a list of best practices, coding standards, and guidelines that are specific to your repo/organization.
 
-The AI model will use this wiki page as a reference, and in case the PR code violates any of the guidelines, it will create additional suggestions, with a dedicated label: `Organization
+The AI model will use this `best_practices.md` file as a reference, and in case the PR code violates any of the guidelines, it will create additional suggestions, with a dedicated label: `Organization
 best practice`.
 
 Example for a python `best_practices.md` content:
@@ -149,16 +149,16 @@ Tips for writing an effective `best_practices.md` file:
     - Long files tend to contain generic guidelines already known to AI
 
 #### Local and global best practices
-By default, Qodo Merge will look for a local `best_practices.md` wiki file in the root of the relevant local repo.
+By default, Qodo Merge will look for a local `best_practices.md` in the root of the relevant local repo.
 
-If you want to enable also a global `best_practices.md` wiki file, set first in the global configuration file:
+If you want to enable also a global `best_practices.md` file, set first in the global configuration file:
 
 ```toml
 [best_practices]
 enable_global_best_practices = true
 ```
 
-Then, create a `best_practices.md` wiki file in the root of [global](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) configuration repository,  `pr-agent-settings`.
+Then, create a `best_practices.md` file in the root of [global](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) configuration repository,  `pr-agent-settings`.
 
 #### Best practices for multiple languages
 For a git organization working with multiple programming languages, you can maintain a centralized global `best_practices.md` file containing language-specific guidelines. 
@@ -191,8 +191,45 @@ And the label will be: `{organization_name} best practice`.
 
 ![best_practice](https://codium.ai/images/pr_agent/org_best_practice.png){width=512}
 
+### Auto best practices
 
-### How to combine `extra instructions` and `best practices`
+>`💎 feature. Platforms supported: GitHub.`
+
+`Auto best practices` is a novel Qodo Merge capability that:
+
+1. Identifies recurring patterns from accepted suggestions
+2. **Automatically** generates [best practices page](https://github.com/qodo-ai/pr-agent/wiki/.pr_agent_auto_best_practices) based on what your team consistently values
+3. Applies these learned patterns to future code reviews
+
+This creates an automatic feedback loop where the system continuously learns from your team's choices to provide increasingly relevant suggestions. 
+The system maintains two analysis phases:
+
+- Open exploration for new issues
+- Targeted checking against established best practices
+
+Note that when a [custom best practices](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) exist, Qodo Merge will still generate an 'auto best practices' wiki file, though it won't use it in the `improve` tool.
+Learn more about utilizing 'auto best practices' in our [detailed guide](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices/).
+
+#### Relevant configurations
+
+```toml
+[auto_best_practices]
+# Disable all auto best practices usage or generation
+enable_auto_best_practices = true  
+
+# Disable usage of auto best practices file in the 'improve' tool
+utilize_auto_best_practices = true 
+
+# Extra instructions to the auto best practices generation prompt
+extra_instructions = ""            
+
+# Max number of patterns to be detected
+max_patterns = 5                   
+```
+
+
+### Combining 'extra instructions' and 'best practices'
+> `💎 feature`
 
 The `extra instructions` configuration is more related to the `improve` tool prompt. It can be used, for example, to avoid specific suggestions ("Don't suggest to add try-except block", "Ignore changes in toml files", ...) or to emphasize specific aspects or formats ("Answer in Japanese", "Give only short suggestions", ...)
 
@@ -231,6 +268,8 @@ dual_publishing_score_threshold = x
 Where x represents the minimum score threshold (>=) for suggestions to be presented as commitable PR comments in addition to the table. Default is -1 (disabled).
 
 ### Self-review
+> `💎 feature` Platforms supported: GitHub, GitLab
+
 If you set in a configuration file:
 ```toml
 [pr_code_suggestions]
@@ -274,20 +313,73 @@ code_suggestions_self_review_text = "... (your text here) ..."
 
         To prevent unauthorized approvals, this configuration defaults to false, and cannot be altered through online comments; enabling requires a direct update to the configuration file and a commit to the repository. This ensures that utilizing the feature demands a deliberate documented decision by the repository owner.
 
+### Auto-approval
+> `💎 feature. Platforms supported: GitHub, GitLab, Bitbucket`
+
+Under specific conditions, Qodo Merge can auto-approve a PR when a specific comment is invoked, or when the PR meets certain criteria.
+
+**To ensure safety, the auto-approval feature is disabled by default.**
+To enable auto-approval features, you need to actively set one or both of the following options in a pre-defined _configuration file_:
+```toml
+[config]
+enable_comment_approval = true # For approval via comments
+enable_auto_approval = true   # For criteria-based auto-approval
+```
+
+!!! note "Notes"
+    - Note that this specific flag cannot be set with a command line argument, only in the configuration file, committed to the repository.
+    - Enabling auto-approval must be a deliberate decision by the repository owner.
+
+1\. **Auto-approval by commenting**
+
+To enable auto-approval by commenting, set in the configuration file:
+```toml
+[config]
+enable_comment_approval = true
+```
+
+After enabling, by commenting on a PR:
+```
+/review auto_approve
+```
+Qodo Merge will automatically approve the PR, and add a comment with the approval.
+
+2\. **Auto-approval when the PR meets certain criteria**
+
+To enable auto-approval based on specific criteria, first, you need to enable the top-level flag:
+```toml
+[config]
+enable_auto_approval = true
+```
+
+There are two criteria that can be set for auto-approval:
+
+- **Review effort score**
+```toml
+[config]
+enable_auto_approval = true
+auto_approve_for_low_review_effort = X # X is a number between 1 to 5
+```
+When the [review effort score](https://www.qodo.ai/images/pr_agent/review3.png) is lower or equal to X, the PR will be auto-approved.
+
+___
+- **No code suggestions**
+```toml
+[config]
+enable_auto_approval = true
+auto_approve_for_no_suggestions = true
+```
+When no [code suggestion](https://www.qodo.ai/images/pr_agent/code_suggestions_as_comment_closed.png) were found for the PR, the PR will be auto-approved.
 
 ### How many code suggestions are generated?
 Qodo Merge uses a dynamic strategy to generate code suggestions based on the size of the pull request (PR). Here's how it works:
 
-1) Chunking large PRs:
-
+#### 1. Chunking large PRs
 - Qodo Merge divides large PRs into 'chunks'.
 - Each chunk contains up to `pr_code_suggestions.max_context_tokens` tokens (default: 14,000).
 
-
-2) Generating suggestions:
-
-- For each chunk, Qodo Merge generates up to `pr_code_suggestions.num_code_suggestions_per_chunk` suggestions (default: 4).
-
+#### 2. Generating suggestions
+- For each chunk, Qodo Merge generates up to `pr_code_suggestions.num_code_suggestions_per_chunk` suggestions (default: 3).
 
 This approach has two main benefits:
 
@@ -320,7 +412,7 @@ Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 line
       </tr>
       <tr>
         <td><b>persistent_comment</b></td>
-        <td>If set to true, the improve comment will be persistent, meaning that every new improve request will edit the previous one. Default is false.</td>
+        <td>If set to true, the improve comment will be persistent, meaning that every new improve request will edit the previous one. Default is true.</td>
       </tr>
       <tr>
         <td><b>suggestions_score_threshold</b></td>
@@ -330,6 +422,10 @@ Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 line
         <td><b>apply_suggestions_checkbox</b></td>
         <td> Enable the checkbox to create a committable suggestion. Default is true.</td>
       </tr>
+      <tr>
+        <td><b>enable_more_suggestions_checkbox</b></td>
+        <td> Enable the checkbox to generate more suggestions. Default is true.</td>
+      </tr>
       <tr>
         <td><b>enable_help_text</b></td>
         <td>If set to true, the tool will display a help text in the comment. Default is true.</td>
@@ -338,13 +434,16 @@ Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 line
         <td><b>enable_chat_text</b></td>
         <td>If set to true, the tool will display a reference to the PR chat in the comment. Default is true.</td>
       </tr>
+      <tr>
+        <td><b>publish_output_no_suggestions</b></td>
+        <td>If set to true, the tool will publish a comment even if no suggestions were found. Default is true.</td>
       <tr>
         <td><b>wiki_page_accepted_suggestions</b></td>
         <td>If set to true, the tool will automatically track accepted suggestions in a dedicated wiki page called `.pr_agent_accepted_suggestions`. Default is true.</td>
       </tr>
       <tr>
         <td><b>allow_thumbs_up_down</b></td>
-        <td>If set to true, all code suggestions will have thumbs up and thumbs down buttons, to encourage users to provide feedback on the suggestions. Default is false.</td>
+        <td>If set to true, all code suggestions will have thumbs up and thumbs down buttons, to encourage users to provide feedback on the suggestions. Default is false. Note that this feature is for statistics tracking. It will not affect future feedback from the AI model.</td>
       </tr>
     </table>
 
@@ -357,7 +456,7 @@ Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 line
       </tr>
       <tr>
         <td><b>num_code_suggestions_per_chunk</b></td>
-        <td>Number of code suggestions provided by the 'improve' tool, per chunk. Default is 4.</td>
+        <td>Number of code suggestions provided by the 'improve' tool, per chunk. Default is 3.</td>
       </tr>
       <tr>
         <td><b>max_number_of_calls</b></td>
@@ -365,14 +464,12 @@ Note: Chunking is primarily relevant for large PRs. For most PRs (up to 500 line
       </tr>
     </table>
 
-## A note on code suggestions quality
+## Understanding AI Code Suggestions
 
-- AI models for code are getting better and better (Sonnet-3.5 and GPT-4), but they are not flawless. Not all the suggestions will be perfect, and a user should not accept all of them automatically. Critical reading and judgment are required.
-- While mistakes of the AI are rare but can happen, a real benefit from the suggestions of the `improve` (and [`review`](https://qodo-merge-docs.qodo.ai/tools/review/)) tool is to catch, with high probability, **mistakes or bugs done by the PR author**, when they happen. So, it's a good practice to spend the needed ~30-60 seconds to review the suggestions, even if not all of them are always relevant.
-- The hierarchical structure of the suggestions is designed to help the user to _quickly_ understand them, and to decide which ones are relevant and which are not:
-
-    - Only if the `Category` header is relevant, the user should move to the summarized suggestion description
-    - Only if the summarized suggestion description is relevant, the user should click on the collapsible, to read the full suggestion description with a code preview example.
-
-- In addition, we recommend to use the [`extra_instructions`](https://qodo-merge-docs.qodo.ai/tools/improve/#extra-instructions-and-best-practices) field to guide the model to suggestions that are more relevant to the specific needs of the project.
-- The interactive [PR chat](https://qodo-merge-docs.qodo.ai/chrome-extension/) also provides an easy way to get more tailored suggestions and feedback from the AI model.
+- **AI Limitations:** AI models for code are getting better and better, but they are not flawless. Not all the suggestions will be perfect, and a user should not accept all of them automatically. Critical reading and judgment are required. Mistakes of the AI are rare but can happen, and it is usually quite easy for a human to spot them.
+- **Purpose of Suggestions:**
+    - **Self-reflection:** The suggestions aim to enable developers to _self-reflect_ and improve their pull requests. This process can help to identify blind spots, uncover missed edge cases, and enhance code readability and coherency. Even when a specific code suggestion isn't suitable, the underlying issue it highlights often reveals something important that might deserve attention.
+    - **Bug detection:** The suggestions also alert on any _critical bugs_ that may have been identified during the analysis. This provides an additional safety net to catch potential issues before they make it into production. It's perfectly acceptable to implement only the suggestions you find valuable for your specific context.
+- **Hierarchy:** Presenting the suggestions in a structured hierarchical table enables the user to _quickly_ understand them, and to decide which ones are relevant and which are not.
+- **Customization:** To guide the model to suggestions that are more relevant to the specific needs of your project, we recommend to use the [`extra_instructions`](https://qodo-merge-docs.qodo.ai/tools/improve/#extra-instructions-and-best-practices) and [`best practices`](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) fields.
+- **Interactive usage:** The interactive [PR chat](https://qodo-merge-docs.qodo.ai/chrome-extension/) also provides an easy way to get more tailored suggestions and feedback from the AI model.

docs/docs/tools/improve_component.md

@@ -18,9 +18,9 @@ The tool will generate code suggestions for the selected component (if no compon
 
 ![improve_component2](https://codium.ai/images/pr_agent/improve_component2.png){width=768}
 
-**Notes**
-- Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
-- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
+!!! note "Notes"
+    - Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
+    - This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
 
 ## Configuration options
 - `num_code_suggestions`: number of code suggestions to provide. Default is 4

docs/docs/tools/index.md

@@ -2,21 +2,21 @@
 
 Here is a list of Qodo Merge tools, each with a dedicated page that explains how to use it:
 
-| Tool                                                                                     | Description                                                                                                                                 |
-|------------------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------|
-| **[PR Description (`/describe`](./describe.md))**                                        | Automatically generating PR description - title, type, summary, code walkthrough and labels                                                 |
-| **[PR Review (`/review`](./review.md))**                                                 | Adjustable feedback about the PR, possible issues, security concerns, review effort and more                                                |
-| **[Code Suggestions (`/improve`](./improve.md))**                                        | Code suggestions for improving the PR                                                                                                       |
-| **[Question Answering (`/ask ...`](./ask.md))**                                          | Answering free-text questions about the PR, or on specific code lines                                                                       |
-| **[Update Changelog (`/update_changelog`](./update_changelog.md))**                      | Automatically updating the CHANGELOG.md file with the PR changes                                                                            |
-| **[Find Similar Issue (`/similar_issue`](./similar_issues.md))**                         | Automatically retrieves and presents similar issues                                                                                         |
-| **[Help (`/help`](./help.md))**                                                          | Provides a list of all the available tools. Also enables to trigger them interactively (💎)                                                 |
-| **💎 [Add Documentation (`/add_docs`](./documentation.md))**                             | Generates documentation to methods/functions/classes that changed in the PR                                                                 |
-| **💎 [Generate Custom Labels (`/generate_labels`](./custom_labels.md))**                 | Generates custom labels for the PR, based on specific guidelines defined by the user                                                        |
-| **💎 [Analyze (`/analyze`](./analyze.md))**                                              | Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component |
-| **💎 [Custom Prompt (`/custom_prompt`](./custom_prompt.md))**                            | Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user                      |
-| **💎 [Generate Tests (`/test component_name`](./test.md))**                              | Automatically generates unit tests for a selected component, based on the PR code changes                                                   |
-| **💎 [Improve Component (`/improve_component component_name`](./improve_component.md))** | Generates code suggestions for a specific code component that changed in the PR                                                             |
-| **💎 [CI Feedback (`/checks ci_job`](./ci_feedback.md))**                                | Automatically generates feedback and analysis for a failed CI job                                                                           |
-
-Note that the tools marked with 💎 are available only for Qodo Merge Pro users.
+| Tool                                                                                     | Description                                                                                                                                |
+|------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------|
+| **[PR Description (`/describe`](./describe.md))**                                        | Automatically generating PR description - title, type, summary, code walkthrough and labels                                                |
+| **[PR Review (`/review`](./review.md))**                                                 | Adjustable feedback about the PR, possible issues, security concerns, review effort and more                                               |
+| **[Code Suggestions (`/improve`](./improve.md))**                                        | Code suggestions for improving the PR                                                                                                      |
+| **[Question Answering (`/ask ...`](./ask.md))**                                          | Answering free-text questions about the PR, or on specific code lines                                                                      |
+| **[Update Changelog (`/update_changelog`](./update_changelog.md))**                      | Automatically updating the CHANGELOG.md file with the PR changes                                                                           |
+| **[Help (`/help`](./help.md))**                                                          | Provides a list of all the available tools. Also enables to trigger them interactively (💎)                                                |
+| **💎 [Add Documentation (`/add_docs`](./documentation.md))**                             | Generates documentation to methods/functions/classes that changed in the PR                                                                |
+| **💎 [Generate Custom Labels (`/generate_labels`](./custom_labels.md))**                 | Generates custom labels for the PR, based on specific guidelines defined by the user                                                       |
+| **💎 [Analyze (`/analyze`](./analyze.md))**                                              | Identify code components that changed in the PR, and enables to interactively generate tests, docs, and code suggestions for each component|
+| **💎 [Test (`/test`](./test.md))**                                                       | generate tests for a selected component, based on the PR code changes                                                                      |
+| **💎 [Custom Prompt (`/custom_prompt`](./custom_prompt.md))**                            | Automatically generates custom suggestions for improving the PR code, based on specific guidelines defined by the user                     |
+| **💎 [Generate Tests (`/test component_name`](./test.md))**                              | Automatically generates unit tests for a selected component, based on the PR code changes                                                  |
+| **💎 [Improve Component (`/improve_component component_name`](./improve_component.md))** | Generates code suggestions for a specific code component that changed in the PR                                                            |
+| **💎 [CI Feedback (`/checks ci_job`](./ci_feedback.md))**                                | Automatically generates feedback and analysis for a failed CI job                                                                          |
+| **💎 [Implement (`/implement`](./implement.md))**                                        | Generates implementation code from review suggestions                                                                                      |
+Note that the tools marked with 💎 are available only for Qodo Merge users.

docs/docs/tools/review.md

@@ -46,133 +46,74 @@ extra_instructions = "..."
 - The `pr_commands` lists commands that will be executed automatically when a PR is opened.
 - The `[pr_reviewer]` section contains the configurations for the `review` tool you want to edit (if any).
 
-[//]: # ()
-[//]: # (### Incremental Mode)
-
-[//]: # (Incremental review only considers changes since the last Qodo Merge review. This can be useful when working on the PR in an iterative manner, and you want to focus on the changes since the last review instead of reviewing the entire PR again.)
-
-[//]: # (For invoking the incremental mode, the following command can be used:)
-
-[//]: # (```)
-
-[//]: # (/review -i)
-
-[//]: # (```)
-
-[//]: # (Note that the incremental mode is only available for GitHub.)
-
-[//]: # ()
-[//]: # (![incremental review](https://codium.ai/images/pr_agent/incremental_review_2.png){width=512})
-
-[//]: # (### PR Reflection)
-
-[//]: # ()
-[//]: # (By invoking:)
-
-[//]: # (```)
-
-[//]: # (/reflect_and_review)
-
-[//]: # (```)
-
-[//]: # (The tool will first ask the author questions about the PR, and will guide the review based on their answers.)
-
-[//]: # ()
-[//]: # (![reflection questions](https://codium.ai/images/pr_agent/reflection_questions.png){width=512})
-
-[//]: # ()
-[//]: # (![reflection answers](https://codium.ai/images/pr_agent/reflection_answers.png){width=512})
-
-[//]: # ()
-[//]: # (![reflection insights](https://codium.ai/images/pr_agent/reflection_insights.png){width=512})
-
-
 
 ## Configuration options
 
 !!! example "General options"
 
-<table>
-  <tr>
-    <td><b>num_code_suggestions</b></td>
-    <td>Number of code suggestions provided by the 'review' tool. Default is 0, meaning no code suggestions will be provided by the `review` tool. Note that this is a legacy feature, that will be removed in future releases. Use the `improve` tool instead for code suggestions</td>
-  </tr>
-  <tr>
-    <td><b>inline_code_comments</b></td>
-    <td>If set to true, the tool will publish the code suggestions as comments on the code diff. Default is false. Note that you need to set `num_code_suggestions`>0 to get code suggestions </td>
-  </tr>
-  <tr>
-    <td><b>persistent_comment</b></td>
-    <td>If set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>extra_instructions</b></td>
-    <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".</td>
-  </tr>
-  <tr>
-    <td><b>enable_help_text</b></td>
-    <td>If set to true, the tool will display a help text in the comment. Default is true.</td>
-  </tr>
-</table>
+    <table>
+      <tr>
+        <td><b>persistent_comment</b></td>
+        <td>If set to true, the review comment will be persistent, meaning that every new review request will edit the previous one. Default is true.</td>
+      </tr>
+      <tr>
+      <td><b>final_update_message</b></td>
+      <td>When set to true, updating a persistent review comment during online commenting will automatically add a short comment with a link to the updated review in the pull request .Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>extra_instructions</b></td>
+        <td>Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...".</td>
+      </tr>
+      <tr>
+        <td><b>enable_help_text</b></td>
+        <td>If set to true, the tool will display a help text in the comment. Default is true.</td>
+      </tr>
+    </table>
 
 !!! example "Enable\\disable specific sub-sections"
 
-<table>
-  <tr>
-    <td><b>require_score_review</b></td>
-    <td>If set to true, the tool will add a section that scores the PR. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>require_tests_review</b></td>
-    <td>If set to true, the tool will add a section that checks if the PR contains tests. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>require_estimate_effort_to_review</b></td>
-    <td>If set to true, the tool will add a section that estimates the effort needed to review the PR. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>require_can_be_split_review</b></td>
-    <td>If set to true, the tool will add a section that checks if the PR contains several themes, and can be split into smaller PRs. Default is false.</td>
-  </tr>
-  <tr>
-    <td><b>require_security_review</b></td>
-    <td>If set to true, the tool will add a section that checks if the PR contains a possible security or vulnerability issue. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>require_ticket_analysis_review</b></td>
-    <td>If set to true, and the PR contains a GitHub or Jira ticket link, the tool will add a section that checks if the PR in fact fulfilled the ticket requirements. Default is true.</td>
-  </tr>
-</table>
+    <table>
+      <tr>
+        <td><b>require_score_review</b></td>
+        <td>If set to true, the tool will add a section that scores the PR. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>require_tests_review</b></td>
+        <td>If set to true, the tool will add a section that checks if the PR contains tests. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>require_estimate_effort_to_review</b></td>
+        <td>If set to true, the tool will add a section that estimates the effort needed to review the PR. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>require_can_be_split_review</b></td>
+        <td>If set to true, the tool will add a section that checks if the PR contains several themes, and can be split into smaller PRs. Default is false.</td>
+      </tr>
+      <tr>
+        <td><b>require_security_review</b></td>
+        <td>If set to true, the tool will add a section that checks if the PR contains a possible security or vulnerability issue. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>require_ticket_analysis_review</b></td>
+        <td>If set to true, and the PR contains a GitHub or Jira ticket link, the tool will add a section that checks if the PR in fact fulfilled the ticket requirements. Default is true.</td>
+      </tr>
+    </table>
 
 !!! example "Adding PR labels"
 
-You can enable\disable the `review` tool to add specific labels to the PR:
+    You can enable\disable the `review` tool to add specific labels to the PR:
 
-<table>
-  <tr>
-    <td><b>enable_review_labels_security</b></td>
-    <td>If set to true, the tool will publish a 'possible security issue' label if it detects a security issue. Default is true.</td>
-  </tr>
-  <tr>
-    <td><b>enable_review_labels_effort</b></td>
-    <td>If set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is true.</td>
-  </tr>
-</table>
+    <table>
+      <tr>
+        <td><b>enable_review_labels_security</b></td>
+        <td>If set to true, the tool will publish a 'possible security issue' label if it detects a security issue. Default is true.</td>
+      </tr>
+      <tr>
+        <td><b>enable_review_labels_effort</b></td>
+        <td>If set to true, the tool will publish a 'Review effort [1-5]: x' label. Default is true.</td>
+      </tr>
+    </table>
 
-!!! example "Auto-approval"
-
-If enabled, the `review` tool can approve a PR when a specific comment, `/review auto_approve`, is invoked.
-
-<table>
-  <tr>
-    <td><b>enable_auto_approval</b></td>
-    <td>If set to true, the tool will approve the PR when invoked with the 'auto_approve' command. Default is false. This flag can be changed only from a configuration file.</td>
-  </tr>
-  <tr>
-    <td><b>maximal_review_effort</b></td>
-    <td>Maximal effort level for auto-approval. If the PR's estimated review effort is above this threshold, the auto-approval will not run. Default is 5.</td>
-  </tr>
-</table>
 
 ## Usage Tips
 
@@ -189,9 +130,9 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
 !!! tip "Automation"
     When you first install Qodo Merge app, the [default mode](../usage-guide/automations_and_usage.md#github-app-automatic-tools-when-a-new-pr-is-opened) for the `review` tool is:
     ```
-    pr_commands = ["/review --pr_reviewer.num_code_suggestions=0", ...]
+    pr_commands = ["/review", ...]
     ```
-    Meaning the `review` tool will run automatically on every PR, without providing code suggestions.
+    Meaning the `review` tool will run automatically on every PR, without any additional configurations.
     Edit this field to enable/disable the tool, or to change the configurations used.
 
 !!! tip "Possible labels from the review tool"
@@ -224,37 +165,10 @@ If enabled, the `review` tool can approve a PR when a specific comment, `/review
     Use triple quotes to write multi-line instructions. Use bullet points to make the instructions more readable.
 
 
-!!! tip "Auto-approval"
-
-    Qodo Merge can approve a PR when a specific comment is invoked.
-
-    To ensure safety, the auto-approval feature is disabled by default. To enable auto-approval, you need to actively set in a pre-defined configuration file the following:
-    ```
-    [pr_reviewer]
-    enable_auto_approval = true
-    ```
-    (this specific flag cannot be set with a command line argument, only in the configuration file, committed to the repository)
 
 
-    After enabling, by commenting on a PR:
-    ```
-    /review auto_approve
-    ```
-    Qodo Merge will automatically approve the PR, and add a comment with the approval.
+!!! tip  "Code suggestions"
 
+    The `review` tool previously included a legacy feature for providing code suggestions (controlled by `--pr_reviewer.num_code_suggestion`). This functionality has been deprecated and replaced by the [`improve`](./improve.md) tool, which offers higher quality and more actionable code suggestions.
 
-    You can also enable auto-approval only if the PR meets certain requirements, such as that the `estimated_review_effort` label is equal or below a certain threshold, by adjusting the flag:
-    ```
-    [pr_reviewer]
-    maximal_review_effort = 5
-    ```
-
-[//]: # (!!! tip  "Code suggestions")
-
-[//]: # ()
-[//]: # (    If you set `num_code_suggestions`>0 , the `review` tool will also provide code suggestions.)
-
-[//]: # (    )
-[//]: # (    Notice If you are interested **only** in the code suggestions, it is recommended to use the [`improve`]&#40;./improve.md&#41; feature instead, since it is a dedicated only to code suggestions, and usually gives better results.)
-
-[//]: # (    Use the `review` tool if you want to get more comprehensive feedback, which includes code suggestions as well.)
+    

docs/docs/tools/similar_issues.md

@@ -16,14 +16,17 @@ It can be invoked manually by commenting on any PR:
 
 Note that to perform retrieval, the `similar_issue` tool indexes all the repo previous issues (once).
 
+### Selecting a Vector Database
+Configure your preferred database by changing the `pr_similar_issue` parameter in `configuration.toml` file.
 
-**Select VectorDBs** by changing `pr_similar_issue` parameter in `configuration.toml` file
+#### Available Options
+Choose from the following Vector Databases:
 
-2 VectorDBs are available to switch in
 1. LanceDB
 2. Pinecone
 
-To enable usage of the '**similar issue**' tool for Pinecone, you need to set the following keys in `.secrets.toml` (or in the relevant environment variables):
+#### Pinecone Configuration
+To use Pinecone with the `similar issue` tool, add these credentials to `.secrets.toml` (or set as environment variables):
 
 ```
 [pinecone]

docs/docs/tools/test.md

@@ -17,9 +17,9 @@ The tool will generate tests for the selected component (if no component is stat
 
 (Example taken from [here](https://github.com/Codium-ai/pr-agent/pull/598#issuecomment-1913679429)):
 
-**Notes**
-- Language that are currently supported by the tool: Python, Java, C++, JavaScript, TypeScript, C#.
-- This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
+!!! note "Notes"
+    - The following languages are currently supported: Python, Java, C++, JavaScript, TypeScript, C#.
+    - This tool can also be triggered interactively by using the [`analyze`](./analyze.md) tool.
 
 
 ## Configuration options

docs/docs/tools/update_changelog.md

@@ -15,5 +15,7 @@ It can be invoked manually by commenting on any PR:
 
 Under the section `pr_update_changelog`, the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L50) contains options to customize the 'update changelog' tool:
 
-- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just print them. Default is false (print only).
-- `extra_instructions`: Optional extra instructions to the tool. For example: "focus on the changes in the file X. Ignore change in ...
+- `push_changelog_changes`: whether to push the changes to CHANGELOG.md, or just publish them as a comment. Default is false (publish as comment).
+- `extra_instructions`: Optional extra instructions to the tool. For example: "Use the following structure: ..."
+- `add_pr_link`: whether the model should try to add a link to the PR in the changelog. Default is true.
+- `skip_ci_on_push`: whether the commit message (when `push_changelog_changes` is true) will include the term "[skip ci]", preventing CI tests to be triggered on the changelog commit. Default is true.

docs/docs/usage-guide/PR_agent_pro_models.md

@@ -1,18 +0,0 @@
-## Qodo Merge Pro Models
-
-The default models used by Qodo Merge Pro are a combination of Claude-3.5-sonnet and  OpenAI's GPT-4 models.
-
-Users can configure Qodo Merge Pro to use solely a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
-
-For example, to restrict Qodo Merge Pro to using only `Claude-3.5-sonnet`, add this setting:
-
-```
-[config]
-model="claude-3-5-sonnet"
-```
-
-Or to restrict Qodo Merge Pro to using only `GPT-4o`, add this setting:
-```
-[config]
-model="gpt-4o"
-```

docs/docs/usage-guide/additional_configurations.md

@@ -1,5 +1,5 @@
 ## Show possible configurations
-The possible configurations of Qodo Merge are stored in [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml).
+The possible configurations of Qodo Merge are stored in [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml){:target="_blank"}.
 In the [tools](https://qodo-merge-docs.qodo.ai/tools/) page you can find explanations on how to use these configurations for each tool.
 
 To print all the available configurations as a comment on your PR, you can use the following command:
@@ -57,16 +57,40 @@ All Qodo Merge tools have a parameter called `extra_instructions`, that enables
 /update_changelog --pr_update_changelog.extra_instructions="Make sure to update also the version ..."
 ```
 
-## Working with large PRs
+## Language Settings
 
-The default mode of CodiumAI is to have a single call per tool, using GPT-4, which has a token limit of 8000 tokens.
-This mode provides a very good speed-quality-cost tradeoff, and can handle most PRs successfully.
-When the PR is above the token limit, it employs a [PR Compression strategy](../core-abilities/index.md).
+The default response language for Qodo Merge is **U.S. English**. However, some development teams may prefer to display information in a different language. For example, your team's workflow might improve if PR descriptions and code suggestions are set to your country's native language.  
 
-However, for very large PRs, or in case you want to emphasize quality over speed and cost, there are two possible solutions:
-1) [Use a model](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/) with larger context, like GPT-32K, or claude-100K. This solution will be applicable for all the tools.
-2) For the `/improve` tool, there is an ['extended' mode](https://qodo-merge-docs.qodo.ai/tools/improve/) (`/improve --extended`),
-which divides the PR into chunks, and processes each chunk separately. With this mode, regardless of the model, no compression will be done (but for large PRs, multiple model calls may occur)
+To configure this, set the `response_language` parameter in the configuration file. This will prompt the model to respond in the specified language. Use a **standard locale code** based on [ISO 3166](https://en.wikipedia.org/wiki/ISO_3166) (country codes) and [ISO 639](https://en.wikipedia.org/wiki/ISO_639) (language codes) to define a language-country pair. See this [comprehensive list of locale codes](https://simplelocalize.io/data/locales/).  
+
+Example: 
+
+```toml
+[config]
+response_language: "it-IT"
+```
+
+This will set the response language globally for all the commands to Italian.
+
+> **Important:** Note that only dynamic text generated by the AI model is translated to the configured language. Static text such as labels and table headers that are not part of the AI models response will remain in US English. In addition, the model you are using must have good support for the specified language. 
+
+[//]: # (## Working with large PRs)
+
+[//]: # ()
+[//]: # (The default mode of CodiumAI is to have a single call per tool, using GPT-4, which has a token limit of 8000 tokens.)
+
+[//]: # (This mode provides a very good speed-quality-cost tradeoff, and can handle most PRs successfully.)
+
+[//]: # (When the PR is above the token limit, it employs a [PR Compression strategy](../core-abilities/index.md).)
+
+[//]: # ()
+[//]: # (However, for very large PRs, or in case you want to emphasize quality over speed and cost, there are two possible solutions:)
+
+[//]: # (1) [Use a model](https://qodo-merge-docs.qodo.ai/usage-guide/changing_a_model/) with larger context, like GPT-32K, or claude-100K. This solution will be applicable for all the tools.)
+
+[//]: # (2) For the `/improve` tool, there is an ['extended' mode](https://qodo-merge-docs.qodo.ai/tools/improve/) (`/improve --extended`),)
+
+[//]: # (which divides the PR into chunks, and processes each chunk separately. With this mode, regardless of the model, no compression will be done (but for large PRs, multiple model calls may occur))
 
 
 
@@ -96,24 +120,16 @@ Increasing this number provides more context to the model, but will also increas
 
 If the PR is too large (see [PR Compression strategy](https://github.com/Codium-ai/pr-agent/blob/main/PR_COMPRESSION.md)), Qodo Merge may automatically set this number to 0, and will use the original git patch.
 
+## Log Level
 
-## Editing the prompts
+Qodo Merge allows you to control the verbosity of logging by using the `log_level` configuration parameter. This is particularly useful for troubleshooting and debugging issues with your PR workflows.
 
-The prompts for the various Qodo Merge tools are defined in the `pr_agent/settings` folder.
-In practice, the prompts are loaded and stored as a standard setting object.
-Hence, editing them is similar to editing any other configuration value - just place the relevant key in `.pr_agent.toml`file, and override the default value.
-
-For example, if you want to edit the prompts of the [describe](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/pr_description_prompts.toml) tool, you can add the following to your `.pr_agent.toml` file:
 ```
-[pr_description_prompt]
-system="""
-...
-"""
-user="""
-...
-"""
+[config]
+log_level = "DEBUG"  # Options: "DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"
 ```
-Note that the new prompt will need to generate an output compatible with the relevant [post-process function](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/tools/pr_description.py#L137).
+
+The default log level is "DEBUG", which provides detailed output of all operations. If you prefer less verbose logs, you can set higher log levels like "INFO" or "WARNING".
 
 ## Integrating with Logging Observability Platforms
 
@@ -138,7 +154,15 @@ LANGSMITH_BASE_URL=<url>
 
 ## Ignoring automatic commands in PRs
 
-In some cases, you may want to automatically ignore specific PRs . Qodo Merge enables you to ignore PR with a specific title, or from/to specific branches (regex matching).
+Qodo Merge allows you to automatically ignore certain PRs based on various criteria:
+
+- PRs with specific titles (using regex matching)
+- PRs between specific branches (using regex matching)
+- PRs not from specific folders
+- PRs containing specific labels
+- PRs opened by specific users
+
+### Ignoring PRs with specific titles
 
 To ignore PRs with a specific title such as "[Bump]: ...", you can add the following to your `configuration.toml` file:
 
@@ -149,6 +173,7 @@ ignore_pr_title = ["\\[Bump\\]"]
 
 Where the `ignore_pr_title` is a list of regex patterns to match the PR title you want to ignore. Default is `ignore_pr_title = ["^\\[Auto\\]", "^Auto"]`.
 
+### Ignoring PRs between specific branches
 
 To ignore PRs from specific source or target branches, you can add the following to your `configuration.toml` file:
 
@@ -161,6 +186,7 @@ ignore_pr_target_branches = ["qa"]
 Where the `ignore_pr_source_branches` and `ignore_pr_target_branches` are lists of regex patterns to match the source and target branches you want to ignore.
 They are not mutually exclusive, you can use them together or separately.
 
+### Ignoring PRs not from specific folders
 
 To allow only specific folders (often needed in large monorepos), set:
 
@@ -169,4 +195,36 @@ To allow only specific folders (often needed in large monorepos), set:
 allow_only_specific_folders=['folder1','folder2']
 ```
 
-For the configuration above, automatic feedback will only be triggered when the PR changes include files from 'folder1' or 'folder2'
+For the configuration above, automatic feedback will only be triggered when the PR changes include files where 'folder1' or 'folder2' is in the file path
+
+### Ignoring PRs containing specific labels
+
+To ignore PRs containing specific labels, you can add the following to your `configuration.toml` file:
+
+``` 
+[config]
+ignore_pr_labels = ["do-not-merge"]
+```
+
+Where the `ignore_pr_labels` is a list of labels that when present in the PR, the PR will be ignored.
+
+### Ignoring PRs from specific users
+
+Qodo Merge automatically identifies and ignores pull requests created by bots using:
+
+- GitHub's native bot detection system
+- Name-based pattern matching
+
+While this detection is robust, it may not catch all cases, particularly when:
+
+- Bots are registered as regular user accounts
+- Bot names don't match common patterns
+
+To supplement the automatic bot detection, you can manually specify users to ignore. Add the following to your `configuration.toml` file to ignore PRs from specific users:
+```
+[config]
+ignore_pr_authors = ["my-special-bot-user", ...]
+```
+
+Where the `ignore_pr_authors` is a list of usernames that you want to ignore.
+

docs/docs/usage-guide/automations_and_usage.md

@@ -7,19 +7,18 @@ Examples of invoking the different tools via the CLI:
 - **Describe**:     `python -m pr_agent.cli --pr_url=<pr_url>  describe`
 - **Improve**:      `python -m pr_agent.cli --pr_url=<pr_url>  improve`
 - **Ask**:          `python -m pr_agent.cli --pr_url=<pr_url>  ask "Write me a poem about this PR"`
-- **Reflect**:      `python -m pr_agent.cli --pr_url=<pr_url>  reflect`
 - **Update Changelog**:      `python -m pr_agent.cli --pr_url=<pr_url>  update_changelog`
 
 `<pr_url>` is the url of the relevant PR (for example: [#50](https://github.com/Codium-ai/pr-agent/pull/50)).
 
 **Notes:**
 
-(1) in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
+1. in addition to editing your local configuration file, you can also change any configuration value by adding it to the command line:
 ```
 python -m pr_agent.cli --pr_url=<pr_url>  /review --pr_reviewer.extra_instructions="focus on the file: ..."
 ```
 
-(2) You can print results locally, without publishing them, by setting in `configuration.toml`:
+2. You can print results locally, without publishing them, by setting in `configuration.toml`:
 ```
 [config]
 publish_output=false
@@ -27,14 +26,9 @@ verbosity_level=2
 ```
 This is useful for debugging or experimenting with different tools.
 
-(3)
+3. **git provider**: The [git_provider](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L5) field in a configuration file determines the GIT provider that will be used by Qodo Merge. Currently, the following providers are supported:
+`github` **(default)**, `gitlab`, `bitbucket`, `azure`, `codecommit`, `local`, and `gerrit`.
 
-**git provider**: The [git_provider](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L5) field in a configuration file determines the GIT provider that will be used by Qodo Merge. Currently, the following providers are supported:
-`
-"github", "gitlab", "bitbucket", "azure", "codecommit", "local", "gerrit"
-`
-
-Default is "github".
 
 ### CLI Health Check
 To verify that Qodo Merge has been configured correctly, you can run this health check command from the repository root:
@@ -67,7 +61,6 @@ Commands for invoking the different tools via comments:
 - **Describe**:     `/describe`
 - **Improve**:      `/improve`  (or `/improve_code` for bitbucket, since `/improve` is sometimes reserved)
 - **Ask**:          `/ask "..."`
-- **Reflect**:      `/reflect`
 - **Update Changelog**:      `/update_changelog`
 
 
@@ -95,8 +88,8 @@ When this parameter is set to `true`, Qodo Merge will not run any automatic tool
 
 ### GitHub App
 
-!!! note "Configurations for Qodo Merge Pro"
-    Qodo Merge Pro for GitHub is an App, hosted by CodiumAI. So all the instructions below are relevant also for Qodo Merge Pro users.
+!!! note "Configurations for Qodo Merge"
+    Qodo Merge for GitHub is an App, hosted by Qodo. So all the instructions below are relevant also for Qodo Merge users.
     Same goes for [GitLab webhook](#gitlab-webhook) and [BitBucket App](#bitbucket-app) sections.
 
 #### GitHub app automatic tools when a new PR is opened
@@ -173,7 +166,7 @@ If not set, the default configuration is `["opened", "reopened", "ready_for_revi
 
 `github_action_config.enable_output` are used to enable/disable github actions [output parameter](https://docs.github.com/en/actions/creating-actions/metadata-syntax-for-github-actions#outputs-for-docker-container-and-javascript-actions) (default is `true`).
 Review result is output as JSON to `steps.{step-id}.outputs.review` property.
-The JSON structure is equivalent to the yaml data structure defined in [pr_reviewer_prompts.toml](https://github.com/idubnori/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml).
+The JSON structure is equivalent to the yaml data structure defined in [pr_reviewer_prompts.toml](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml).
 
 Note that you can give additional config parameters by adding environment variables to `.github/workflows/pr_agent.yml`, or by using a `.pr_agent.toml` [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file) in the root of your repo
 
@@ -213,9 +206,9 @@ push_commands = [
 Note that to use the 'handle_push_trigger' feature, you need to give the gitlab webhook also the "Push events" scope.
 
 ### BitBucket App
-Similar to GitHub app, when running Qodo Merge from BitBucket App, the default [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) from a pre-built docker will be initially loaded.
+Similar to GitHub app, when running Qodo Merge from BitBucket App, the default [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml) will be initially loaded.
 
-By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+By uploading a local `.pr_agent.toml` file to the root of the repo's default branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
 
 For example, if your local `.pr_agent.toml` file contains:
 ```toml
@@ -285,7 +278,7 @@ To control which commands will run automatically when a new PR is opened, you ca
 [azure_devops_server]
 pr_commands = [
     "/describe",
-    "/review --pr_reviewer.num_code_suggestions=0",
+    "/review",
     "/improve",
 ]
 ```

docs/docs/usage-guide/changing_a_model.md

@@ -1,20 +1,26 @@
-## Changing a model
+## Changing a model in PR-Agent
 
 See [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/__init__.py) for a list of available models.
-To use a different model than the default (GPT-4), you need to edit in the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L2) the fields:
-```
+To use a different model than the default (o3-mini), you need to edit in the [configuration file](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/settings/configuration.toml#L2) the fields:
+
+```toml
 [config]
 model = "..."
 fallback_models = ["..."]
 ```
 
 For models and environments not from OpenAI, you might need to provide additional keys and other parameters.
-You can give parameters via a configuration file (see below for instructions), or from environment variables. See [litellm documentation](https://litellm.vercel.app/docs/proxy/quick_start#supported-llms) for the environment variables relevant per model.
+You can give parameters via a configuration file, or from environment variables.
+
+!!! note "Model-specific environment variables"
+    See [litellm documentation](https://litellm.vercel.app/docs/proxy/quick_start#supported-llms) for the environment variables needed per model, as they may vary and change over time. Our documentation per-model may not always be up-to-date with the latest changes.
+    Failing to set the needed keys of a specific model will usually result in litellm not identifying the model type, and failing to utilize it.
 
 ### Azure
 
 To use Azure, set in your `.secrets.toml` (working from CLI), or in the GitHub `Settings > Secrets and variables` (working from GitHub App or GitHub Action):
-```
+
+```toml
 [openai]
 key = "" # your azure api key
 api_type = "azure"
@@ -24,95 +30,130 @@ deployment_id = ""  # The deployment name you chose when you deployed the engine
 ```
 
 and set in your configuration file:
-```
+
+```toml
 [config]
 model="" # the OpenAI model you've deployed on Azure (e.g. gpt-4o)
 fallback_models=["..."]
 ```
 
+To use Azure AD (Entra id) based authentication set in your `.secrets.toml` (working from CLI), or in the GitHub `Settings > Secrets and variables` (working from GitHub App or GitHub Action):
+
+```toml
+[azure_ad]
+client_id = ""  # Your Azure AD application client ID
+client_secret = ""  # Your Azure AD application client secret
+tenant_id = ""  # Your Azure AD tenant ID
+api_base = ""  # Your Azure OpenAI service base URL (e.g., https://openai.xyz.com/)
+```
+
+
+Passing custom headers to the underlying LLM Model API can be done by setting extra_headers parameter to litellm.
+
+```toml
+[litellm]
+extra_headers='{"projectId": "<authorized projectId >", ...}') #The value of this setting should be a JSON string representing the desired headers, a ValueError is thrown otherwise.
+```
+
+This enables users to pass authorization tokens or API keys, when routing requests through an API management gateway.
+
+### Ollama
+
+You can run models locally through either [VLLM](https://docs.litellm.ai/docs/providers/vllm) or [Ollama](https://docs.litellm.ai/docs/providers/ollama)
+
+E.g. to use a new model locally via Ollama, set in `.secrets.toml` or in a configuration file:
+
+```toml
+[config]
+model = "ollama/qwen2.5-coder:32b"
+fallback_models=["ollama/qwen2.5-coder:32b"]
+custom_model_max_tokens=128000 # set the maximal input tokens for the model
+duplicate_examples=true # will duplicate the examples in the prompt, to help the model to generate structured output
+
+[ollama]
+api_base = "http://localhost:11434" # or whatever port you're running Ollama on
+```
+
+By default, Ollama uses a context window size of 2048 tokens. In most cases this is not enough to cover pr-agent promt and pull-request diff. Context window size can be overridden with the `OLLAMA_CONTEXT_LENGTH` environment variable. For example, to set the default context length to 8K, use: `OLLAMA_CONTEXT_LENGTH=8192 ollama serve`. More information you can find on the [official ollama faq](https://github.com/ollama/ollama/blob/main/docs/faq.md#how-can-i-specify-the-context-window-size).
+
+Please note that the `custom_model_max_tokens` setting should be configured in accordance with the `OLLAMA_CONTEXT_LENGTH`. Failure to do so may result in unexpected model output.
+
+!!! note "Local models vs commercial models"
+    Qodo Merge is compatible with almost any AI model, but analyzing complex code repositories and pull requests requires a model specifically optimized for code analysis.
+
+    Commercial models such as GPT-4, Claude Sonnet, and Gemini have demonstrated robust capabilities in generating structured output for code analysis tasks with large input. In contrast, most open-source models currently available (as of January 2025) face challenges with these complex tasks.
+
+    Based on our testing, local open-source models are suitable for experimentation and learning purposes (mainly for the `ask` command), but they are not suitable for production-level code analysis tasks.
+    
+    Hence, for production workflows and real-world usage, we recommend using commercial models.
+
 ### Hugging Face
 
-**Local**
-You can run Hugging Face models locally through either [VLLM](https://docs.litellm.ai/docs/providers/vllm) or [Ollama](https://docs.litellm.ai/docs/providers/ollama)
-
-E.g. to use a new Hugging Face model locally via Ollama, set:
-```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-ollama": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "ollama/llama2": 4096
-}
-
-
-[config] # in configuration.toml
-model = "ollama/llama2"
-fallback_models=["ollama/llama2"]
-
-[ollama] # in .secrets.toml
-api_base = ... # the base url for your Hugging Face inference endpoint
-# e.g. if running Ollama locally, you may use:
-api_base = "http://localhost:11434/"
-```
-
-### Inference Endpoints
-
 To use a new model with Hugging Face Inference Endpoints, for example, set:
-```
-[__init__.py]
-MAX_TOKENS = {
-    "model-name-on-huggingface": <max_tokens>
-}
-e.g.
-MAX_TOKENS={
-    ...,
-    "meta-llama/Llama-2-7b-chat-hf": 4096
-}
+
+```toml
 [config] # in configuration.toml
 model = "huggingface/meta-llama/Llama-2-7b-chat-hf"
 fallback_models=["huggingface/meta-llama/Llama-2-7b-chat-hf"]
+custom_model_max_tokens=... # set the maximal input tokens for the model
 
 [huggingface] # in .secrets.toml
 key = ... # your Hugging Face api key
 api_base = ... # the base url for your Hugging Face inference endpoint
 ```
+
 (you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
 
 ### Replicate
 
 To use Llama2 model with Replicate, for example, set:
-```
+
+```toml
 [config] # in configuration.toml
 model = "replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"
 fallback_models=["replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1"]
 [replicate] # in .secrets.toml
 key = ...
 ```
-(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
 
+(you can obtain a Llama2 key from [here](https://replicate.com/replicate/llama-2-70b-chat/api))
 
 Also, review the [AiHandler](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/ai_handler.py) file for instructions on how to set keys for other models.
 
 ### Groq
 
 To use Llama3 model with Groq, for example, set:
-```
+
+```toml
 [config] # in configuration.toml
 model = "llama3-70b-8192"
 fallback_models = ["groq/llama3-70b-8192"]
 [groq] # in .secrets.toml
 key = ... # your Groq api key
 ```
+
 (you can obtain a Groq key from [here](https://console.groq.com/keys))
 
+### xAI
+
+To use xAI's models with PR-Agent, set:
+
+```toml
+[config] # in configuration.toml
+model = "xai/grok-2-latest"
+fallback_models = ["xai/grok-2-latest"] # or any other model as fallback
+
+[xai] # in .secrets.toml
+key = "..." # your xAI API key
+```
+
+You can obtain an xAI API key from [xAI's console](https://console.x.ai/) by creating an account and navigating to the developer settings page.
+
 ### Vertex AI
 
 To use Google's Vertex AI platform and its associated models (chat-bison/codechat-bison) set:
 
-```
+```toml
 [config] # in configuration.toml
 model = "vertex_ai/codechat-bison"
 fallback_models="vertex_ai/codechat-bison"
@@ -145,51 +186,111 @@ If you don't want to set the API key in the .secrets.toml file, you can set the
 
 To use Anthropic models, set the relevant models in the configuration section of the configuration file:
 
-```
+```toml
 [config]
 model="anthropic/claude-3-opus-20240229"
 fallback_models=["anthropic/claude-3-opus-20240229"]
 ```
 
 And also set the api key in the .secrets.toml file:
-```
+
+```toml
 [anthropic]
 KEY = "..."
 ```
 
+See [litellm](https://docs.litellm.ai/docs/providers/anthropic#usage) documentation for more information about the environment variables required for Anthropic.
+
 ### Amazon Bedrock
 
 To use Amazon Bedrock and its foundational models, add the below configuration:
 
-```
+```toml
 [config] # in configuration.toml
-model="bedrock/anthropic.claude-3-sonnet-20240229-v1:0"
-fallback_models=["bedrock/anthropic.claude-v2:1"]
+model="bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0"
+fallback_models=["bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0"]
+
+[aws]
+AWS_ACCESS_KEY_ID="..."
+AWS_SECRET_ACCESS_KEY="..."
+AWS_REGION_NAME="..."
 ```
 
-Note that you have to add access to foundational models before using them. Please refer to [this document](https://docs.aws.amazon.com/bedrock/latest/userguide/setting-up.html) for more details.
+See [litellm](https://docs.litellm.ai/docs/providers/bedrock#usage) documentation for more information about the environment variables required for Amazon Bedrock.
 
-If you are using the claude-3 model, please configure the following settings as there are parameters incompatible with claude-3.
-```
-[litellm]
-drop_params = true
+### DeepSeek
+
+To use deepseek-chat model with DeepSeek, for example, set:
+
+```toml
+[config] # in configuration.toml
+model = "deepseek/deepseek-chat"
+fallback_models=["deepseek/deepseek-chat"]
 ```
 
-AWS session is automatically authenticated from your environment, but you can also explicitly set `AWS_ACCESS_KEY_ID`, `AWS_SECRET_ACCESS_KEY` and `AWS_REGION_NAME` environment variables. Please refer to [this document](https://litellm.vercel.app/docs/providers/bedrock) for more details.
+and fill up your key
+
+```toml
+[deepseek] # in .secrets.toml
+key = ...
+```
+
+(you can obtain a deepseek-chat key from [here](https://platform.deepseek.com))
+
+### DeepInfra
+
+To use DeepSeek model with DeepInfra, for example, set:
+
+```toml
+[config] # in configuration.toml
+model = "deepinfra/deepseek-ai/DeepSeek-R1-Distill-Llama-70B"
+fallback_models = ["deepinfra/deepseek-ai/DeepSeek-R1-Distill-Qwen-32B"]
+[deepinfra] # in .secrets.toml
+key = ... # your DeepInfra api key
+```
+
+(you can obtain a DeepInfra key from [here](https://deepinfra.com/dash/api_keys))
 
 ### Custom models
 
 If the relevant model doesn't appear [here](https://github.com/Codium-ai/pr-agent/blob/main/pr_agent/algo/__init__.py), you can still use it as a custom model:
 
-(1) Set the model name in the configuration file:
-```
+1. Set the model name in the configuration file:
+
+```toml
 [config]
 model="custom_model_name"
 fallback_models=["custom_model_name"]
 ```
-(2) Set the maximal tokens for the model:
-```
+
+2. Set the maximal tokens for the model:
+
+```toml
 [config]
 custom_model_max_tokens= ...
 ```
-(3) Go to [litellm documentation](https://litellm.vercel.app/docs/proxy/quick_start#supported-llms), find the model you want to use, and set the relevant environment variables.
+
+3. Go to [litellm documentation](https://litellm.vercel.app/docs/proxy/quick_start#supported-llms), find the model you want to use, and set the relevant environment variables.
+
+4. Most reasoning models do not support chat-style inputs (`system` and `user` messages) or temperature settings.
+To bypass chat templates and temperature controls, set `config.custom_reasoning_model = true` in your configuration file.
+
+## Dedicated parameters
+
+### OpenAI models
+
+```toml
+[config]
+reasoning_efffort= = "medium" # "low", "medium", "high"
+```
+
+With the OpenAI models that support reasoning effort (eg: o3-mini), you can specify its reasoning effort via `config` section. The default value is `medium`. You can change it to `high` or `low` based on your usage.
+
+### Anthropic models
+
+```toml
+[config]
+enable_claude_extended_thinking = false # Set to true to enable extended thinking feature
+extended_thinking_budget_tokens = 2048
+extended_thinking_max_output_tokens = 4096
+```

docs/docs/usage-guide/configuration_options.md

@@ -20,7 +20,7 @@ In terms of precedence, wiki configurations will override local configurations,
 
 `Platforms supported: GitHub, GitLab, Bitbucket`
 
-With Qodo Merge Pro, you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo.
+With Qodo Merge, you can set configurations by creating a page called `.pr_agent.toml` in the [wiki](https://github.com/Codium-ai/pr-agent/wiki/pr_agent.toml) of the repo.
 The advantage of this method is that it allows to set configurations without needing to commit new content to the repo - just edit the wiki page and **save**.
 
 
@@ -41,7 +41,7 @@ Qodo Merge will know to remove the surrounding quotes when reading the configura
 `Platforms supported: GitHub, GitLab, Bitbucket, Azure DevOps`
 
 
-By uploading a local `.pr_agent.toml` file to the root of the repo's main branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
+By uploading a local `.pr_agent.toml` file to the root of the repo's default branch, you can edit and customize any configuration parameter. Note that you need to upload `.pr_agent.toml` prior to creating a PR, in order for the configuration to take effect.
 
 For example, if you set in `.pr_agent.toml`:
 
@@ -61,7 +61,7 @@ Then you can give a list of extra instructions to the `review` tool.
 
 `Platforms supported: GitHub, GitLab, Bitbucket`
 
-If you create a repo called `pr-agent-settings` in your **organization**, it's configuration file `.pr_agent.toml` will be used as a global configuration file for any other repo that belongs to the same organization.
+If you create a repo called `pr-agent-settings` in your **organization**, its configuration file `.pr_agent.toml` will be used as a global configuration file for any other repo that belongs to the same organization.
 Parameters from a local `.pr_agent.toml` file, in a specific repo, will override the global configuration parameters.
 
 For example, in the GitHub organization `Codium-ai`:
@@ -69,3 +69,29 @@ For example, in the GitHub organization `Codium-ai`:
 - The file [`https://github.com/Codium-ai/pr-agent-settings/.pr_agent.toml`](https://github.com/Codium-ai/pr-agent-settings/blob/main/.pr_agent.toml)  serves as a global configuration file for all the repos in the GitHub organization `Codium-ai`.
 
 - The repo [`https://github.com/Codium-ai/pr-agent`](https://github.com/Codium-ai/pr-agent/blob/main/.pr_agent.toml) inherits the global configuration file from `pr-agent-settings`.
+
+### Bitbucket Organization level configuration file 💎
+`Relevant platforms: Bitbucket Data Center`
+
+In Bitbucket Data Center, there are two levels where you can define a global configuration file:
+
+* Project-level global configuration:
+
+Create a repository named `pr-agent-settings` within a specific project. The configuration file in this repository will apply to all repositories under the same project.
+
+* Organization-level global configuration:
+
+Create a dedicated project to hold a global configuration file that affects all repositories across all projects in your organization.
+
+**Setting up organization-level global configuration:**
+
+1.	Create a new project with both the name and key: PR_AGENT_SETTINGS.
+2.	Inside the PR_AGENT_SETTINGS project, create a repository named pr-agent-settings.
+3.	In this repository, add a `.pr_agent.toml` configuration file—structured similarly to the global configuration file described above.
+4.	Optionally, you can add organizational-level [global best practices file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#global-configuration-file).
+
+Repositories across your entire Bitbucket organization will inherit the configuration from this file.
+
+!!! note "Note"
+    If both organization-level and project-level global settings are defined, the project-level settings will take precedence over the organization-level configuration. Additionally, parameters from a repository’s local .pr_agent.toml file will always override both global settings.
+

docs/docs/usage-guide/enabling_a_wiki.md

@@ -0,0 +1,32 @@
+`Supported Git Platforms: GitHub, GitLab, Bitbucket`
+
+
+For optimal functionality of Qodo Merge, we recommend enabling a wiki for each repository where Qodo Merge is installed. The wiki serves several important purposes:
+
+**Key Wiki Features: 💎**
+
+- Storing a [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#wiki-configuration-file)
+- Track [accepted suggestions](https://qodo-merge-docs.qodo.ai/tools/improve/#suggestion-tracking)
+- Facilitates learning over time by creating an [auto_best_practices.md](https://qodo-merge-docs.qodo.ai/core-abilities/auto_best_practices) file
+
+
+**Setup Instructions (GitHub):**
+
+To enable a wiki for your repository:
+
+1. Navigate to your repository's main page on GitHub
+2. Select "Settings" from the top navigation bar
+3. Locate the "Features" section
+4. Enable the "Wikis" option by checking the corresponding box
+5. Return to your repository's main page
+6. Look for the newly added "Wiki" tab in the top navigation
+7. Initialize your wiki by clicking "Create the first page" and saving (this step is important - without creating an initial page, the wiki will not be fully functional)
+
+### Why Wiki?
+
+- Your code (and its derivatives, including accepted code suggestions) is yours. Qodo Merge will never store it on external servers.
+- Repository changes typically require pull requests, which create overhead and are time-consuming. This process is too cumbersome for auto data aggregation, and is not very convenient even for managing frequently updated content like configuration files.
+- A repository wiki page provides an ideal balance:
+    - It lives within your repository, making it suitable for code-related documentation
+    - It enables quick updates without the overhead of pull requests
+    - It maintains full Git version control, allowing you to track changes over time.

docs/docs/usage-guide/index.md

@@ -5,6 +5,7 @@ It includes information on how to adjust Qodo Merge configurations, define which
 
 
 - [Introduction](./introduction.md)
+- [Enabling a Wiki](./enabling_a_wiki)
 - [Configuration File](./configuration_options.md)
 - [Usage and Automation](./automations_and_usage.md)
     - [Local Repo (CLI)](./automations_and_usage.md#local-repo-cli)
@@ -22,5 +23,4 @@ It includes information on how to adjust Qodo Merge configurations, define which
     - [Working with large PRs](./additional_configurations.md#working-with-large-prs)
     - [Changing a model](./additional_configurations.md#changing-a-model)
     - [Patch Extra Lines](./additional_configurations.md#patch-extra-lines)
-    - [Editing the prompts](./additional_configurations.md#editing-the-prompts)
-- [Qodo Merge Pro Models](./PR_agent_pro_models.md)
+- [Qodo Merge Models](./qodo_merge_models)

docs/docs/usage-guide/introduction.md

@@ -2,7 +2,7 @@
 After [installation](https://qodo-merge-docs.qodo.ai/installation/), there are three basic ways to invoke Qodo Merge:
 
 1. Locally running a CLI command
-2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901) on a PR
+2. Online usage - by [commenting](https://github.com/Codium-ai/pr-agent/pull/229#issuecomment-1695021901){:target="_blank"} on a PR
 3. Enabling Qodo Merge tools to run automatically when a new PR is opened
 
 

docs/docs/usage-guide/qodo_merge_models.md

@@ -0,0 +1,32 @@
+
+The default model used by Qodo Merge (March 2025) is Claude Sonnet 3.7.
+
+### Selecting a Specific Model
+
+Users can configure Qodo Merge to use a specific model by editing the [configuration](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/) file.
+The models supported by Qodo Merge are:
+
+- `claude-3-7-sonnet` (default)
+- `o3-mini`
+- `gpt-4.1`
+- `deepseek/r1`
+
+To restrict Qodo Merge to using only `o3-mini`, add this setting:
+```
+[config]
+model="o3-mini"
+```
+
+To restrict Qodo Merge to using only `GPT-4.1`, add this setting:
+```
+[config]
+model="gpt-4.1"
+```
+
+To restrict Qodo Merge to using only `deepseek-r1` us-hosted, add this setting:
+```
+[config]
+model="deepseek/r1"
+```
+
+

docs/mkdocs.yml

@@ -1,29 +1,26 @@
-site_name: Qodo Merge (formerly known as PR-Agent)
-repo_url: https://github.com/Codium-ai/pr-agent
-repo_name: Codium-ai/pr-agent
+site_name: Qodo Merge (and open-source PR-Agent)
+repo_url: https://github.com/qodo-ai/pr-agent
+repo_name: Qodo-ai/pr-agent
 
 nav:
   - Overview:
     - 'index.md'
-    - 💎 Qodo Merge Pro: 'overview/pr_agent_pro.md'
+    - 💎 Qodo Merge: 'overview/pr_agent_pro.md'
     - Data Privacy: 'overview/data_privacy.md'
   - Installation:
     - 'installation/index.md'
-    - Locally: 'installation/locally.md'
-    - GitHub: 'installation/github.md'
-    - GitLab: 'installation/gitlab.md'
-    - BitBucket: 'installation/bitbucket.md'
-    - Azure DevOps: 'installation/azure.md'
-    - 💎 Qodo Merge Pro: 'installation/pr_agent_pro.md'
+    - PR-Agent: 'installation/pr_agent.md'
+    - 💎 Qodo Merge: 'installation/qodo_merge.md'
   - Usage Guide:
     - 'usage-guide/index.md'
     - Introduction: 'usage-guide/introduction.md'
+    - Enabling a Wiki: 'usage-guide/enabling_a_wiki.md'
     - Configuration File: 'usage-guide/configuration_options.md'
     - Usage and Automation: 'usage-guide/automations_and_usage.md'
     - Managing Mail Notifications: 'usage-guide/mail_notifications.md'
     - Changing a Model: 'usage-guide/changing_a_model.md'
     - Additional Configurations: 'usage-guide/additional_configurations.md'
-    - 💎 Qodo Merge Pro Models: 'usage-guide/PR_agent_pro_models'
+    - 💎 Qodo Merge Models: 'usage-guide/qodo_merge_models.md'
   - Tools:
     - 'tools/index.md'
     - Describe: 'tools/describe.md'
@@ -31,7 +28,7 @@ nav:
     - Improve: 'tools/improve.md'
     - Ask: 'tools/ask.md'
     - Update Changelog: 'tools/update_changelog.md'
-    - Similar Issues: 'tools/similar_issues.md'
+    - Help Docs: 'tools/help_docs.md'
     - Help: 'tools/help.md'
     - 💎 Analyze: 'tools/analyze.md'
     - 💎 Test: 'tools/test.md'
@@ -41,24 +38,29 @@ nav:
     - 💎 Custom Prompt: 'tools/custom_prompt.md'
     - 💎 CI Feedback: 'tools/ci_feedback.md'
     - 💎 Similar Code: 'tools/similar_code.md'
+    - 💎 Implement: 'tools/implement.md'
   - Core Abilities:
       - 'core-abilities/index.md'
-      - Fetching ticket context: 'core-abilities/fetching_ticket_context.md'
-      - Local and global metadata: 'core-abilities/metadata.md'
+      - Auto best practices: 'core-abilities/auto_best_practices.md'
+      - Pull request benchmark: 'finetuning_benchmark/index.md'
+      - Code validation: 'core-abilities/code_validation.md'
+      - Compression strategy: 'core-abilities/compression_strategy.md'
       - Dynamic context: 'core-abilities/dynamic_context.md'
-      - Self-reflection: 'core-abilities/self_reflection.md'
+      - Fetching ticket context: 'core-abilities/fetching_ticket_context.md'
       - Impact evaluation: 'core-abilities/impact_evaluation.md'
       - Interactivity: 'core-abilities/interactivity.md'
-      - Compression strategy: 'core-abilities/compression_strategy.md'
-      - Code-oriented YAML: 'core-abilities/code_oriented_yaml.md'
+      - Local and global metadata: 'core-abilities/metadata.md'
+      - RAG context enrichment: 'core-abilities/rag_context_enrichment.md'
+      - Self-reflection: 'core-abilities/self_reflection.md'
       - Static code analysis: 'core-abilities/static_code_analysis.md'
-      - Code Fine-tuning Benchmark: 'finetuning_benchmark/index.md'
   - Chrome Extension:
       - Qodo Merge Chrome Extension: 'chrome-extension/index.md'
       - Features: 'chrome-extension/features.md'
       - Data Privacy: 'chrome-extension/data_privacy.md'
+      - Options: 'chrome-extension/options.md'
   - FAQ:
       - FAQ: 'faq/index.md'
+  - AI Docs Search: 'ai_search/index.md'
 #  - Code Fine-tuning Benchmark: 'finetuning_benchmark/index.md'
 
 theme:
@@ -154,4 +156,4 @@ markdown_extensions:
 
 
 copyright: |
-  &copy; 2024 <a href="https://www.codium.ai/"  target="_blank" rel="noopener">CodiumAI</a>
+  &copy; 2025 <a href="https://www.codium.ai/"  target="_blank" rel="noopener">QodoAI</a>

docs/overrides/partials/footer.html

@@ -82,7 +82,7 @@
 
 <footer class="wrapper">
   <div class="container">
-    <p class="footer-text">© 2024 <a href="https://www.qodo.ai/" target="_blank" rel="noopener">Qodo</a></p>
+    <p class="footer-text">© 2025 <a href="https://www.qodo.ai/" target="_blank" rel="noopener">Qodo</a></p>
     <div class="footer-links">
       <a href="https://qodo-gen-docs.qodo.ai/">Qodo Gen</a>
       <p>|</p>

pr_agent/agent/pr_agent.py

@@ -3,6 +3,7 @@ from functools import partial
 
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
 from pr_agent.algo.ai_handlers.litellm_ai_handler import LiteLLMAIHandler
+from pr_agent.algo.cli_args import CliArgs
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
@@ -12,8 +13,8 @@ from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
 from pr_agent.tools.pr_config import PRConfig
 from pr_agent.tools.pr_description import PRDescription
 from pr_agent.tools.pr_generate_labels import PRGenerateLabels
+from pr_agent.tools.pr_help_docs import PRHelpDocs
 from pr_agent.tools.pr_help_message import PRHelpMessage
-from pr_agent.tools.pr_information_from_user import PRInformationFromUser
 from pr_agent.tools.pr_line_questions import PR_LineQuestions
 from pr_agent.tools.pr_questions import PRQuestions
 from pr_agent.tools.pr_reviewer import PRReviewer
@@ -25,8 +26,6 @@ command2class = {
     "answer": PRReviewer,
     "review": PRReviewer,
     "review_pr": PRReviewer,
-    "reflect": PRInformationFromUser,
-    "reflect_and_review": PRInformationFromUser,
     "describe": PRDescription,
     "describe_pr": PRDescription,
     "improve": PRCodeSuggestions,
@@ -41,15 +40,16 @@ command2class = {
     "similar_issue": PRSimilarIssue,
     "add_docs": PRAddDocs,
     "generate_labels": PRGenerateLabels,
+    "help_docs": PRHelpDocs,
 }
 
 commands = list(command2class.keys())
 
 
+
 class PRAgent:
     def __init__(self, ai_handler: partial[BaseAiHandler,] = LiteLLMAIHandler):
         self.ai_handler = ai_handler  # will be initialized in run_action
-        self.forbidden_cli_args = ['enable_auto_approval']
 
     async def handle_request(self, pr_url, request, notify=None) -> bool:
         # First, apply repo specific settings if exists
@@ -64,24 +64,37 @@ class PRAgent:
         else:
             action, *args = request
 
-        if args:
-            for forbidden_arg in self.forbidden_cli_args:
-                for arg in args:
-                    if forbidden_arg in arg:
-                        get_logger().error(
-                            f"CLI argument for param '{forbidden_arg}' is forbidden. Use instead a configuration file."
-                        )
-                        return False
+        # validate args
+        is_valid, arg = CliArgs.validate_user_args(args)
+        if not is_valid:
+            get_logger().error(
+                f"CLI argument for param '{arg}' is forbidden. Use instead a configuration file."
+            )
+            return False
+
+        # Update settings from args
         args = update_settings_from_args(args)
 
+        # Append the response language in the extra instructions
+        response_language = get_settings().config.get('response_language', 'en-us')
+        if response_language.lower() != 'en-us':
+            get_logger().info(f'User has set the response language to: {response_language}')
+            for key in get_settings():
+                setting = get_settings().get(key)
+                if str(type(setting)) == "<class 'dynaconf.utils.boxing.DynaBox'>":
+                    if hasattr(setting, 'extra_instructions'):
+                        current_extra_instructions = setting.extra_instructions
+                        if current_extra_instructions:
+                            setting.extra_instructions = current_extra_instructions+ f"\n======\n\nIn addition, Your response MUST be written in the language corresponding to local code: {response_language}. This is crucial."
+                        else:
+                            setting.extra_instructions = f"Your response MUST be written in the language corresponding to locale code: '{response_language}'. This is crucial."
+
         action = action.lstrip("/").lower()
         if action not in command2class:
-            get_logger().debug(f"Unknown command: {action}")
+            get_logger().warning(f"Unknown command: {action}")
             return False
         with get_logger().contextualize(command=action, pr_url=pr_url):
             get_logger().info("PR-Agent request handler started", analytics=True)
-            if action == "reflect_and_review":
-                get_settings().pr_reviewer.ask_and_reflect = True
             if action == "answer":
                 if notify:
                     notify()

pr_agent/algo/__init__.py

@@ -20,15 +20,27 @@ MAX_TOKENS = {
     'gpt-4o-mini-2024-07-18': 128000,  # 128K, but may be limited by config.max_model_tokens
     'gpt-4o-2024-08-06': 128000,  # 128K, but may be limited by config.max_model_tokens
     'gpt-4o-2024-11-20': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4.5-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4.5-preview-2025-02-27': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'gpt-4.1': 1047576,
+    'gpt-4.1-2025-04-14': 1047576,
+    'gpt-4.1-mini': 1047576,
+    'gpt-4.1-mini-2025-04-14': 1047576,
+    'gpt-4.1-nano': 1047576,
+    'gpt-4.1-nano-2025-04-14': 1047576,
     'o1-mini': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-mini-2024-09-12': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-preview': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-preview-2024-09-12': 128000,  # 128K, but may be limited by config.max_model_tokens
     'o1-2024-12-17': 204800,  # 200K, but may be limited by config.max_model_tokens
     'o1': 204800,  # 200K, but may be limited by config.max_model_tokens
+    'o3-mini': 204800,  # 200K, but may be limited by config.max_model_tokens
+    'o3-mini-2025-01-31': 204800,  # 200K, but may be limited by config.max_model_tokens
     'claude-instant-1': 100000,
     'claude-2': 100000,
     'command-nightly': 4096,
+    'deepseek/deepseek-chat': 128000,  # 128K, but may be limited by config.max_model_tokens
+    'deepseek/deepseek-reasoner': 64000,  # 64K, but may be limited by config.max_model_tokens
     'replicate/llama-2-70b-chat:2c1608e18606fad2812020dc541930f2d0495ce32eee50074220b87300bc16e1': 4096,
     'meta-llama/Llama-2-7b-chat-hf': 4096,
     'vertex_ai/codechat-bison': 6144,
@@ -39,12 +51,15 @@ MAX_TOKENS = {
     'vertex_ai/claude-3-opus@20240229': 100000,
     'vertex_ai/claude-3-5-sonnet@20240620': 100000,
     'vertex_ai/claude-3-5-sonnet-v2@20241022': 100000,
+    'vertex_ai/claude-3-7-sonnet@20250219': 200000,
     'vertex_ai/gemini-1.5-pro': 1048576,
     'vertex_ai/gemini-1.5-flash': 1048576,
+    'vertex_ai/gemini-2.0-flash': 1048576,
     'vertex_ai/gemma2': 8200,
     'gemini/gemini-1.5-pro': 1048576,
     'gemini/gemini-1.5-flash': 1048576,
-    'gemini/gemini-2.0-flash-exp': 1048576,
+    'gemini/gemini-2.0-flash': 1048576,
+    'gemini/gemini-2.5-pro-preview-03-25': 1048576,
     'codechat-bison': 6144,
     'codechat-bison-32k': 32000,
     'anthropic.claude-instant-v1': 100000,
@@ -53,6 +68,8 @@ MAX_TOKENS = {
     'anthropic/claude-3-opus-20240229': 100000,
     'anthropic/claude-3-5-sonnet-20240620': 100000,
     'anthropic/claude-3-5-sonnet-20241022': 100000,
+    'anthropic/claude-3-7-sonnet-20250219': 200000,
+    'claude-3-7-sonnet-20250219': 200000,
     'anthropic/claude-3-5-haiku-20241022': 100000,
     'bedrock/anthropic.claude-instant-v1': 100000,
     'bedrock/anthropic.claude-v2': 100000,
@@ -62,13 +79,25 @@ MAX_TOKENS = {
     'bedrock/anthropic.claude-3-5-haiku-20241022-v1:0': 100000,
     'bedrock/anthropic.claude-3-5-sonnet-20240620-v1:0': 100000,
     'bedrock/anthropic.claude-3-5-sonnet-20241022-v2:0': 100000,
+    'bedrock/anthropic.claude-3-7-sonnet-20250219-v1:0': 200000,
+    "bedrock/us.anthropic.claude-3-5-sonnet-20241022-v2:0": 100000,
+    "bedrock/us.anthropic.claude-3-7-sonnet-20250219-v1:0": 200000,
     'claude-3-5-sonnet': 100000,
+    'groq/meta-llama/llama-4-scout-17b-16e-instruct': 131072,
+    'groq/meta-llama/llama-4-maverick-17b-128e-instruct': 131072,
     'groq/llama3-8b-8192': 8192,
     'groq/llama3-70b-8192': 8192,
+    'groq/llama-3.1-8b-instant': 8192,
+    'groq/llama-3.3-70b-versatile': 128000,
     'groq/mixtral-8x7b-32768': 32768,
-    'groq/llama-3.1-8b-instant': 131072,
-    'groq/llama-3.1-70b-versatile': 131072,
-    'groq/llama-3.1-405b-reasoning': 131072,
+    'groq/gemma2-9b-it': 8192,
+    'xai/grok-2': 131072,
+    'xai/grok-2-1212': 131072,
+    'xai/grok-2-latest': 131072,
+    'xai/grok-3-beta': 131072,
+    'xai/grok-3-fast-beta': 131072,
+    'xai/grok-3-mini-beta': 131072,
+    'xai/grok-3-mini-fast-beta': 131072,
     'ollama/llama3': 4096,
     'watsonx/meta-llama/llama-3-8b-instruct': 4096,
     "watsonx/meta-llama/llama-3-70b-instruct": 4096,
@@ -76,4 +105,35 @@ MAX_TOKENS = {
     "watsonx/ibm/granite-13b-chat-v2": 8191,
     "watsonx/ibm/granite-34b-code-instruct": 8191,
     "watsonx/mistralai/mistral-large": 32768,
+    "deepinfra/deepseek-ai/DeepSeek-R1-Distill-Qwen-32B": 128000,
+    "deepinfra/deepseek-ai/DeepSeek-R1-Distill-Llama-70B": 128000,
+    "deepinfra/deepseek-ai/DeepSeek-R1": 128000,
 }
+
+USER_MESSAGE_ONLY_MODELS = [
+    "deepseek/deepseek-reasoner",
+    "o1-mini",
+    "o1-mini-2024-09-12",
+    "o1-preview"
+]
+
+NO_SUPPORT_TEMPERATURE_MODELS = [
+    "deepseek/deepseek-reasoner",
+    "o1-mini",
+    "o1-mini-2024-09-12",
+    "o1",
+    "o1-2024-12-17",
+    "o3-mini",
+    "o3-mini-2025-01-31",
+    "o1-preview"
+]
+
+SUPPORT_REASONING_EFFORT_MODELS = [
+    "o3-mini",
+    "o3-mini-2025-01-31"
+]
+
+CLAUDE_EXTENDED_THINKING_MODELS = [
+    "anthropic/claude-3-7-sonnet-20250219",
+    "claude-3-7-sonnet-20250219"
+]

pr_agent/algo/ai_handlers/litellm_ai_handler.py

@@ -1,15 +1,16 @@
 import os
-
 import litellm
 import openai
 import requests
 from litellm import acompletion
 from tenacity import retry, retry_if_exception_type, stop_after_attempt
 
+from pr_agent.algo import CLAUDE_EXTENDED_THINKING_MODELS, NO_SUPPORT_TEMPERATURE_MODELS, SUPPORT_REASONING_EFFORT_MODELS, USER_MESSAGE_ONLY_MODELS
 from pr_agent.algo.ai_handlers.base_ai_handler import BaseAiHandler
-from pr_agent.algo.utils import get_version
+from pr_agent.algo.utils import ReasoningEffort, get_version
 from pr_agent.config_loader import get_settings
 from pr_agent.log import get_logger
+import json
 
 OPENAI_RETRIES = 5
 
@@ -29,6 +30,7 @@ class LiteLLMAIHandler(BaseAiHandler):
         self.azure = False
         self.api_base = None
         self.repetition_penalty = None
+        
         if get_settings().get("OPENAI.KEY", None):
             openai.api_key = get_settings().openai.key
             litellm.openai_key = get_settings().openai.key
@@ -39,11 +41,6 @@ class LiteLLMAIHandler(BaseAiHandler):
             os.environ["AWS_ACCESS_KEY_ID"] = get_settings().aws.AWS_ACCESS_KEY_ID
             os.environ["AWS_SECRET_ACCESS_KEY"] = get_settings().aws.AWS_SECRET_ACCESS_KEY
             os.environ["AWS_REGION_NAME"] = get_settings().aws.AWS_REGION_NAME
-        if get_settings().get("litellm.use_client"):
-            litellm_token = get_settings().get("litellm.LITELLM_TOKEN")
-            assert litellm_token, "LITELLM_TOKEN is required"
-            os.environ["LITELLM_TOKEN"] = litellm_token
-            litellm.use_client = True
         if get_settings().get("LITELLM.DROP_PARAMS", None):
             litellm.drop_params = get_settings().litellm.drop_params
         if get_settings().get("LITELLM.SUCCESS_CALLBACK", None):
@@ -70,6 +67,8 @@ class LiteLLMAIHandler(BaseAiHandler):
             litellm.api_key = get_settings().groq.key
         if get_settings().get("REPLICATE.KEY", None):
             litellm.replicate_key = get_settings().replicate.key
+        if get_settings().get("XAI.KEY", None):
+            litellm.api_key = get_settings().xai.key
         if get_settings().get("HUGGINGFACE.KEY", None):
             litellm.huggingface_key = get_settings().huggingface.key
         if get_settings().get("HUGGINGFACE.API_BASE", None) and 'huggingface' in get_settings().config.model:
@@ -90,6 +89,59 @@ class LiteLLMAIHandler(BaseAiHandler):
         if get_settings().get("GOOGLE_AI_STUDIO.GEMINI_API_KEY", None):
           os.environ["GEMINI_API_KEY"] = get_settings().google_ai_studio.gemini_api_key
 
+        # Support deepseek models
+        if get_settings().get("DEEPSEEK.KEY", None):
+            os.environ['DEEPSEEK_API_KEY'] = get_settings().get("DEEPSEEK.KEY")
+
+        # Support deepinfra models
+        if get_settings().get("DEEPINFRA.KEY", None):
+            os.environ['DEEPINFRA_API_KEY'] = get_settings().get("DEEPINFRA.KEY")
+
+        # Check for Azure AD configuration
+        if get_settings().get("AZURE_AD.CLIENT_ID", None):
+            self.azure = True
+            # Generate access token using Azure AD credentials from settings
+            access_token = self._get_azure_ad_token()
+            litellm.api_key = access_token
+            openai.api_key = access_token
+            
+            # Set API base from settings
+            self.api_base = get_settings().azure_ad.api_base
+            litellm.api_base = self.api_base
+            openai.api_base = self.api_base
+
+        # Models that only use user meessage
+        self.user_message_only_models = USER_MESSAGE_ONLY_MODELS
+
+        # Model that doesn't support temperature argument
+        self.no_support_temperature_models = NO_SUPPORT_TEMPERATURE_MODELS
+
+        # Models that support reasoning effort
+        self.support_reasoning_models = SUPPORT_REASONING_EFFORT_MODELS
+
+        # Models that support extended thinking
+        self.claude_extended_thinking_models = CLAUDE_EXTENDED_THINKING_MODELS
+
+    def _get_azure_ad_token(self):
+        """
+        Generates an access token using Azure AD credentials from settings.
+        Returns:
+            str: The access token
+        """
+        from azure.identity import ClientSecretCredential
+        try:
+            credential = ClientSecretCredential(
+                tenant_id=get_settings().azure_ad.tenant_id,
+                client_id=get_settings().azure_ad.client_id,
+                client_secret=get_settings().azure_ad.client_secret
+            )
+            # Get token for Azure OpenAI service
+            token = credential.get_token("https://cognitiveservices.azure.com/.default")
+            return token.token
+        except Exception as e:
+            get_logger().error(f"Failed to get Azure AD token: {e}")
+            raise
+
     def prepare_logs(self, response, system, user, resp, finish_reason):
         response_log = response.dict().copy()
         response_log['system'] = system
@@ -102,6 +154,43 @@ class LiteLLMAIHandler(BaseAiHandler):
             response_log['main_pr_language'] = 'unknown'
         return response_log
 
+    def _configure_claude_extended_thinking(self, model: str, kwargs: dict) -> dict:
+        """
+        Configure Claude extended thinking parameters if applicable.
+
+        Args:
+            model (str): The AI model being used
+            kwargs (dict): The keyword arguments for the model call
+
+        Returns:
+            dict: Updated kwargs with extended thinking configuration
+        """
+        extended_thinking_budget_tokens = get_settings().config.get("extended_thinking_budget_tokens", 2048)
+        extended_thinking_max_output_tokens = get_settings().config.get("extended_thinking_max_output_tokens", 4096)
+
+        # Validate extended thinking parameters
+        if not isinstance(extended_thinking_budget_tokens, int) or extended_thinking_budget_tokens <= 0:
+            raise ValueError(f"extended_thinking_budget_tokens must be a positive integer, got {extended_thinking_budget_tokens}")
+        if not isinstance(extended_thinking_max_output_tokens, int) or extended_thinking_max_output_tokens <= 0:
+            raise ValueError(f"extended_thinking_max_output_tokens must be a positive integer, got {extended_thinking_max_output_tokens}")
+        if extended_thinking_max_output_tokens < extended_thinking_budget_tokens:
+            raise ValueError(f"extended_thinking_max_output_tokens ({extended_thinking_max_output_tokens}) must be greater than or equal to extended_thinking_budget_tokens ({extended_thinking_budget_tokens})")
+
+        kwargs["thinking"] = {
+            "type": "enabled",
+            "budget_tokens": extended_thinking_budget_tokens
+        }
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info(f"Adding max output tokens {extended_thinking_max_output_tokens} to model {model}, extended thinking budget tokens: {extended_thinking_budget_tokens}")
+        kwargs["max_tokens"] = extended_thinking_max_output_tokens
+
+        # temperature may only be set to 1 when thinking is enabled
+        if get_settings().config.verbosity_level >= 2:
+            get_logger().info("Temperature may only be set to 1 when thinking is enabled with claude models.")
+        kwargs["temperature"] = 1
+
+        return kwargs
+
     def add_litellm_callbacks(selfs, kwargs) -> dict:
         captured_extra = []
 
@@ -193,13 +282,11 @@ class LiteLLMAIHandler(BaseAiHandler):
                 messages[1]["content"] = [{"type": "text", "text": messages[1]["content"]},
                                           {"type": "image_url", "image_url": {"url": img_path}}]
 
-            # Currently, model OpenAI o1 series does not support a separate system and user prompts
-            O1_MODEL_PREFIX = 'o1'
-            model_type = model.split('/')[-1] if '/' in model else model
-            if model_type.startswith(O1_MODEL_PREFIX):
+            # Currently, some models do not support a separate system and user prompts
+            if model in self.user_message_only_models or get_settings().config.custom_reasoning_model:
                 user = f"{system}\n\n\n{user}"
                 system = ""
-                get_logger().info(f"Using O1 model, combining system and user prompts")
+                get_logger().info(f"Using model {model}, combining system and user prompts")
                 messages = [{"role": "user", "content": user}]
                 kwargs = {
                     "model": model,
@@ -213,11 +300,26 @@ class LiteLLMAIHandler(BaseAiHandler):
                     "model": model,
                     "deployment_id": deployment_id,
                     "messages": messages,
-                    "temperature": temperature,
                     "timeout": get_settings().config.ai_timeout,
                     "api_base": self.api_base,
                 }
 
+            # Add temperature only if model supports it
+            if model not in self.no_support_temperature_models and not get_settings().config.custom_reasoning_model:
+                # get_logger().info(f"Adding temperature with value {temperature} to model {model}.")
+                kwargs["temperature"] = temperature
+
+            # Add reasoning_effort if model supports it
+            if (model in self.support_reasoning_models):
+                supported_reasoning_efforts = [ReasoningEffort.HIGH.value, ReasoningEffort.MEDIUM.value, ReasoningEffort.LOW.value]
+                reasoning_effort = get_settings().config.reasoning_effort if (get_settings().config.reasoning_effort in supported_reasoning_efforts) else ReasoningEffort.MEDIUM.value
+                get_logger().info(f"Adding reasoning_effort with value {reasoning_effort} to model {model}.")
+                kwargs["reasoning_effort"] = reasoning_effort
+
+            # https://docs.anthropic.com/en/docs/build-with-claude/extended-thinking
+            if (model in self.claude_extended_thinking_models) and get_settings().config.get("enable_claude_extended_thinking", False):
+                kwargs = self._configure_claude_extended_thinking(model, kwargs)
+
             if get_settings().litellm.get("enable_callbacks", False):
                 kwargs = self.add_litellm_callbacks(kwargs)
 
@@ -231,6 +333,16 @@ class LiteLLMAIHandler(BaseAiHandler):
             if self.repetition_penalty:
                 kwargs["repetition_penalty"] = self.repetition_penalty
 
+            #Added support for extra_headers while using litellm to call underlying model, via a api management gateway, would allow for passing custom headers for security and authorization
+            if get_settings().get("LITELLM.EXTRA_HEADERS", None):
+                try:
+                    litellm_extra_headers = json.loads(get_settings().litellm.extra_headers)
+                    if not isinstance(litellm_extra_headers, dict):
+                        raise ValueError("LITELLM.EXTRA_HEADERS must be a JSON object")
+                except json.JSONDecodeError as e:
+                    raise ValueError(f"LITELLM.EXTRA_HEADERS contains invalid JSON: {str(e)}")
+                kwargs["extra_headers"] = litellm_extra_headers
+
             get_logger().debug("Prompts", artifact={"system": system, "user": user})
 
             if get_settings().config.verbosity_level >= 2:

pr_agent/algo/cli_args.py

@@ -0,0 +1,36 @@
+from base64 import b64decode, encode, b64encode
+import hashlib
+
+class CliArgs:
+    @staticmethod
+    def validate_user_args(args: list) -> (bool, str):
+        try:
+            if not args:
+                return True, ""
+
+            # decode forbidden args
+            # b64encode('word'.encode()).decode()
+            _encoded_args = 'c2hhcmVkX3NlY3JldA==:dXNlcg==:c3lzdGVt:ZW5hYmxlX2NvbW1lbnRfYXBwcm92YWw=:ZW5hYmxlX21hbnVhbF9hcHByb3ZhbA==:ZW5hYmxlX2F1dG9fYXBwcm92YWw=:YXBwcm92ZV9wcl9vbl9zZWxmX3Jldmlldw==:YmFzZV91cmw=:dXJs:YXBwX25hbWU=:c2VjcmV0X3Byb3ZpZGVy:Z2l0X3Byb3ZpZGVy:c2tpcF9rZXlz:b3BlbmFpLmtleQ==:QU5BTFlUSUNTX0ZPTERFUg==:dXJp:YXBwX2lk:d2ViaG9va19zZWNyZXQ=:YmVhcmVyX3Rva2Vu:UEVSU09OQUxfQUNDRVNTX1RPS0VO:b3ZlcnJpZGVfZGVwbG95bWVudF90eXBl:cHJpdmF0ZV9rZXk=:bG9jYWxfY2FjaGVfcGF0aA==:ZW5hYmxlX2xvY2FsX2NhY2hl:amlyYV9iYXNlX3VybA==:YXBpX2Jhc2U=:YXBpX3R5cGU=:YXBpX3ZlcnNpb24=:c2tpcF9rZXlz'
+
+            forbidden_cli_args = []
+            for e in _encoded_args.split(':'):
+                forbidden_cli_args.append(b64decode(e).decode())
+
+            # lowercase all forbidden args
+            for i, _ in enumerate(forbidden_cli_args):
+                forbidden_cli_args[i] = forbidden_cli_args[i].lower()
+                if '.' not in forbidden_cli_args[i]:
+                    forbidden_cli_args[i] = '.' + forbidden_cli_args[i]
+
+            for arg in args:
+                if arg.startswith('--'):
+                    arg_word = arg.lower()
+                    arg_word = arg_word.replace('__', '.')  # replace double underscore with dot, e.g. --openai__key -> --openai.key
+                    for forbidden_arg_word in forbidden_cli_args:
+                        if forbidden_arg_word in arg_word:
+                            return False, forbidden_arg_word
+            return True, ""
+        except Exception as e:
+            return False, str(e)
+
+

pr_agent/algo/git_patch_processing.py

@@ -9,11 +9,12 @@ from pr_agent.log import get_logger
 
 
 def extend_patch(original_file_str, patch_str, patch_extra_lines_before=0,
-                 patch_extra_lines_after=0, filename: str = "") -> str:
+                 patch_extra_lines_after=0, filename: str = "", new_file_str="") -> str:
     if not patch_str or (patch_extra_lines_before == 0 and patch_extra_lines_after == 0) or not original_file_str:
         return patch_str
 
     original_file_str = decode_if_bytes(original_file_str)
+    new_file_str = decode_if_bytes(new_file_str)
     if not original_file_str:
         return patch_str
 
@@ -22,7 +23,7 @@ def extend_patch(original_file_str, patch_str, patch_extra_lines_before=0,
 
     try:
         extended_patch_str = process_patch_lines(patch_str, original_file_str,
-                                                 patch_extra_lines_before, patch_extra_lines_after)
+                                                 patch_extra_lines_before, patch_extra_lines_after, new_file_str)
     except Exception as e:
         get_logger().warning(f"Failed to extend patch: {e}", artifact={"traceback": traceback.format_exc()})
         return patch_str
@@ -52,12 +53,13 @@ def should_skip_patch(filename):
     return False
 
 
-def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before, patch_extra_lines_after):
+def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before, patch_extra_lines_after, new_file_str=""):
     allow_dynamic_context = get_settings().config.allow_dynamic_context
     patch_extra_lines_before_dynamic = get_settings().config.max_extra_lines_before_dynamic_context
 
-    original_lines = original_file_str.splitlines()
-    len_original_lines = len(original_lines)
+    file_original_lines = original_file_str.splitlines()
+    file_new_lines = new_file_str.splitlines() if new_file_str else []
+    len_original_lines = len(file_original_lines)
     patch_lines = patch_str.splitlines()
     extended_patch_lines = []
 
@@ -73,12 +75,12 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
                 if match:
                     # finish processing previous hunk
                     if is_valid_hunk and (start1 != -1 and patch_extra_lines_after > 0):
-                        delta_lines = [f' {line}' for line in original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]]
-                        extended_patch_lines.extend(delta_lines)
+                        delta_lines_original = [f' {line}' for line in file_original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]]
+                        extended_patch_lines.extend(delta_lines_original)
 
                     section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
 
-                    is_valid_hunk = check_if_hunk_lines_matches_to_file(i, original_lines, patch_lines, start1)
+                    is_valid_hunk = check_if_hunk_lines_matches_to_file(i, file_original_lines, patch_lines, start1)
 
                     if is_valid_hunk and (patch_extra_lines_before > 0 or patch_extra_lines_after > 0):
                         def _calc_context_limits(patch_lines_before):
@@ -93,20 +95,28 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
                                 extended_size2 = max(extended_size2 - delta_cap, size2)
                             return extended_start1, extended_size1, extended_start2, extended_size2
 
-                        if allow_dynamic_context:
+                        if allow_dynamic_context and file_new_lines:
                             extended_start1, extended_size1, extended_start2, extended_size2 = \
                                 _calc_context_limits(patch_extra_lines_before_dynamic)
-                            lines_before = original_lines[extended_start1 - 1:start1 - 1]
+
+                            lines_before_original = file_original_lines[extended_start1 - 1:start1 - 1]
+                            lines_before_new = file_new_lines[extended_start2 - 1:start2 - 1]
                             found_header = False
-                            for i, line, in enumerate(lines_before):
-                                if section_header in line:
-                                    found_header = True
-                                    # Update start and size in one line each
-                                    extended_start1, extended_start2 = extended_start1 + i, extended_start2 + i
-                                    extended_size1, extended_size2 = extended_size1 - i, extended_size2 - i
-                                    # get_logger().debug(f"Found section header in line {i} before the hunk")
-                                    section_header = ''
-                                    break
+                            if lines_before_original == lines_before_new: # Making sure no changes from a previous hunk
+                                for i, line, in enumerate(lines_before_original):
+                                    if section_header in line:
+                                        found_header = True
+                                        # Update start and size in one line each
+                                        extended_start1, extended_start2 = extended_start1 + i, extended_start2 + i
+                                        extended_size1, extended_size2 = extended_size1 - i, extended_size2 - i
+                                        # get_logger().debug(f"Found section header in line {i} before the hunk")
+                                        section_header = ''
+                                        break
+                            else:
+                                get_logger().debug(f"Extra lines before hunk are different in original and new file - dynamic context",
+                                                   artifact={"lines_before_original": lines_before_original,
+                                                             "lines_before_new": lines_before_new})
+
                             if not found_header:
                                 # get_logger().debug(f"Section header not found in the extra lines before the hunk")
                                 extended_start1, extended_size1, extended_start2, extended_size2 = \
@@ -115,11 +125,23 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
                             extended_start1, extended_size1, extended_start2, extended_size2 = \
                                 _calc_context_limits(patch_extra_lines_before)
 
-                        delta_lines = [f' {line}' for line in original_lines[extended_start1 - 1:start1 - 1]]
+                        # check if extra lines before hunk are different in original and new file
+                        delta_lines_original = [f' {line}' for line in file_original_lines[extended_start1 - 1:start1 - 1]]
+                        if file_new_lines:
+                            delta_lines_new = [f' {line}' for line in file_new_lines[extended_start2 - 1:start2 - 1]]
+                            if delta_lines_original != delta_lines_new:
+                                get_logger().debug(f"Extra lines before hunk are different in original and new file",
+                                                   artifact={"delta_lines_original": delta_lines_original,
+                                                             "delta_lines_new": delta_lines_new})
+                                extended_start1 = start1
+                                extended_size1 = size1
+                                extended_start2 = start2
+                                extended_size2 = size2
+                                delta_lines_original = []
 
                         #  logic to remove section header if its in the extra delta lines (in dynamic context, this is also done)
                         if section_header and not allow_dynamic_context:
-                            for line in delta_lines:
+                            for line in delta_lines_original:
                                 if section_header in line:
                                     section_header = ''  # remove section header if it is in the extra delta lines
                                     break
@@ -128,12 +150,12 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
                         extended_size1 = size1
                         extended_start2 = start2
                         extended_size2 = size2
-                        delta_lines = []
+                        delta_lines_original = []
                     extended_patch_lines.append('')
                     extended_patch_lines.append(
                         f'@@ -{extended_start1},{extended_size1} '
                         f'+{extended_start2},{extended_size2} @@ {section_header}')
-                    extended_patch_lines.extend(delta_lines)  # one to zero based
+                    extended_patch_lines.extend(delta_lines_original)  # one to zero based
                     continue
             extended_patch_lines.append(line)
     except Exception as e:
@@ -142,15 +164,14 @@ def process_patch_lines(patch_str, original_file_str, patch_extra_lines_before,
 
     # finish processing last hunk
     if start1 != -1 and patch_extra_lines_after > 0 and is_valid_hunk:
-        delta_lines = original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]
+        delta_lines_original = file_original_lines[start1 + size1 - 1:start1 + size1 - 1 + patch_extra_lines_after]
         # add space at the beginning of each extra line
-        delta_lines = [f' {line}' for line in delta_lines]
-        extended_patch_lines.extend(delta_lines)
+        delta_lines_original = [f' {line}' for line in delta_lines_original]
+        extended_patch_lines.extend(delta_lines_original)
 
     extended_patch_str = '\n'.join(extended_patch_lines)
     return extended_patch_str
 
-
 def check_if_hunk_lines_matches_to_file(i, original_lines, patch_lines, start1):
     """
     Check if the hunk lines match the original file content. We saw cases where the hunk header line doesn't match the original file content, and then
@@ -160,8 +181,18 @@ def check_if_hunk_lines_matches_to_file(i, original_lines, patch_lines, start1):
     try:
         if i + 1 < len(patch_lines) and patch_lines[i + 1][0] == ' ': # an existing line in the file
             if patch_lines[i + 1].strip() != original_lines[start1 - 1].strip():
+                # check if different encoding is needed
+                original_line = original_lines[start1 - 1].strip()
+                for encoding in ['iso-8859-1', 'latin-1', 'ascii', 'utf-16']:
+                    try:
+                        if original_line.encode(encoding).decode().strip() == patch_lines[i + 1].strip():
+                            get_logger().info(f"Detected different encoding in hunk header line {start1}, needed encoding: {encoding}")
+                            return False # we still want to avoid extending the hunk. But we don't want to log an error
+                    except:
+                        pass
+
                 is_valid_hunk = False
-                get_logger().error(
+                get_logger().info(
                     f"Invalid hunk in PR, line {start1} in hunk header doesn't match the original file content")
     except:
         pass
@@ -254,7 +285,7 @@ def handle_patch_deletions(patch: str, original_file_content_str: str,
     return patch
 
 
-def convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
+def decouple_and_convert_to_hunks_with_lines_numbers(patch: str, file) -> str:
     """
     Convert a given patch string into a string with line numbers for each hunk, indicating the new and old content of
     the file.
@@ -286,11 +317,17 @@ __old hunk__
         line6
            ...
     """
-    # if the file was deleted, return a message indicating that the file was deleted
-    if hasattr(file, 'edit_type') and file.edit_type == EDIT_TYPE.DELETED:
-        return f"\n\n## file '{file.filename.strip()}' was deleted\n"
 
-    patch_with_lines_str = f"\n\n## File: '{file.filename.strip()}'\n"
+    # Add a header for the file
+    if file:
+        # if the file was deleted, return a message indicating that the file was deleted
+        if hasattr(file, 'edit_type') and file.edit_type == EDIT_TYPE.DELETED:
+            return f"\n\n## File '{file.filename.strip()}' was deleted\n"
+
+        patch_with_lines_str = f"\n\n## File: '{file.filename.strip()}'\n"
+    else:
+        patch_with_lines_str = ""
+
     patch_lines = patch.splitlines()
     RE_HUNK_HEADER = re.compile(
         r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
@@ -363,49 +400,56 @@ __old hunk__
     return patch_with_lines_str.rstrip()
 
 
-def extract_hunk_lines_from_patch(patch: str, file_name, line_start, line_end, side) -> tuple[str, str]:
+def extract_hunk_lines_from_patch(patch: str, file_name, line_start, line_end, side, remove_trailing_chars: bool = True) -> tuple[str, str]:
+    try:
+        patch_with_lines_str = f"\n\n## File: '{file_name.strip()}'\n\n"
+        selected_lines = ""
+        patch_lines = patch.splitlines()
+        RE_HUNK_HEADER = re.compile(
+            r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
+        match = None
+        start1, size1, start2, size2 = -1, -1, -1, -1
+        skip_hunk = False
+        selected_lines_num = 0
+        for line in patch_lines:
+            if 'no newline at end of file' in line.lower():
+                continue
 
-    patch_with_lines_str = f"\n\n## File: '{file_name.strip()}'\n\n"
-    selected_lines = ""
-    patch_lines = patch.splitlines()
-    RE_HUNK_HEADER = re.compile(
-        r"^@@ -(\d+)(?:,(\d+))? \+(\d+)(?:,(\d+))? @@[ ]?(.*)")
-    match = None
-    start1, size1, start2, size2 = -1, -1, -1, -1
-    skip_hunk = False
-    selected_lines_num = 0
-    for line in patch_lines:
-        if 'no newline at end of file' in line.lower():
-            continue
+            if line.startswith('@@'):
+                skip_hunk = False
+                selected_lines_num = 0
+                header_line = line
 
-        if line.startswith('@@'):
-            skip_hunk = False
-            selected_lines_num = 0
-            header_line = line
+                match = RE_HUNK_HEADER.match(line)
 
-            match = RE_HUNK_HEADER.match(line)
+                section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
 
-            section_header, size1, size2, start1, start2 = extract_hunk_headers(match)
-
-            # check if line range is in this hunk
-            if side.lower() == 'left':
                 # check if line range is in this hunk
-                if not (start1 <= line_start <= start1 + size1):
-                    skip_hunk = True
-                    continue
-            elif side.lower() == 'right':
-                if not (start2 <= line_start <= start2 + size2):
-                    skip_hunk = True
-                    continue
-            patch_with_lines_str += f'\n{header_line}\n'
+                if side.lower() == 'left':
+                    # check if line range is in this hunk
+                    if not (start1 <= line_start <= start1 + size1):
+                        skip_hunk = True
+                        continue
+                elif side.lower() == 'right':
+                    if not (start2 <= line_start <= start2 + size2):
+                        skip_hunk = True
+                        continue
+                patch_with_lines_str += f'\n{header_line}\n'
 
-        elif not skip_hunk:
-            if side.lower() == 'right' and line_start <= start2 + selected_lines_num <= line_end:
-                selected_lines += line + '\n'
-            if side.lower() == 'left' and start1 <= selected_lines_num + start1 <= line_end:
-                selected_lines += line + '\n'
-            patch_with_lines_str += line + '\n'
-            if not line.startswith('-'): # currently we don't support /ask line for deleted lines
-                selected_lines_num += 1
+            elif not skip_hunk:
+                if side.lower() == 'right' and line_start <= start2 + selected_lines_num <= line_end:
+                    selected_lines += line + '\n'
+                if side.lower() == 'left' and start1 <= selected_lines_num + start1 <= line_end:
+                    selected_lines += line + '\n'
+                patch_with_lines_str += line + '\n'
+                if not line.startswith('-'): # currently we don't support /ask line for deleted lines
+                    selected_lines_num += 1
+    except Exception as e:
+        get_logger().error(f"Failed to extract hunk lines from patch: {e}", artifact={"traceback": traceback.format_exc()})
+        return "", ""
 
-    return patch_with_lines_str.rstrip(), selected_lines.rstrip()
+    if remove_trailing_chars:
+        patch_with_lines_str = patch_with_lines_str.rstrip()
+        selected_lines = selected_lines.rstrip()
+
+    return patch_with_lines_str, selected_lines

pr_agent/algo/language_handler.py

@@ -19,6 +19,12 @@ def is_valid_file(filename:str, bad_extensions=None) -> bool:
         bad_extensions = get_settings().bad_extensions.default
         if get_settings().config.use_extra_bad_extensions:
             bad_extensions += get_settings().bad_extensions.extra
+
+    auto_generated_files = ['package-lock.json', 'yarn.lock', 'composer.lock', 'Gemfile.lock', 'poetry.lock']
+    for forbidden_file in auto_generated_files:
+        if filename.endswith(forbidden_file):
+            return False
+
     return filename.split('.')[-1] not in bad_extensions
 
 
@@ -41,6 +47,7 @@ def sort_files_by_main_languages(languages: Dict, files: list):
 
     # filter out files bad extensions
     files_filtered = filter_bad_extensions(files)
+
     # sort files by their extension, put the files that are in the main extension first
     # and the rest files after, map languages_sorted to their respective files
     files_sorted = []

pr_agent/algo/pr_processing.py

@@ -7,7 +7,8 @@ from github import RateLimitExceededException
 
 from pr_agent.algo.file_filter import filter_ignored
 from pr_agent.algo.git_patch_processing import (
-    convert_to_hunks_with_lines_numbers, extend_patch, handle_patch_deletions)
+    extend_patch, handle_patch_deletions,
+    decouple_and_convert_to_hunks_with_lines_numbers)
 from pr_agent.algo.language_handler import sort_files_by_main_languages
 from pr_agent.algo.token_handler import TokenHandler
 from pr_agent.algo.types import EDIT_TYPE, FilePatchInfo
@@ -50,22 +51,11 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler,
         PATCH_EXTRA_LINES_AFTER = cap_and_log_extra_lines(PATCH_EXTRA_LINES_AFTER, "after")
 
     try:
-        diff_files_original = git_provider.get_diff_files()
+        diff_files = git_provider.get_diff_files()
     except RateLimitExceededException as e:
         get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
 
-    diff_files = filter_ignored(diff_files_original)
-    if diff_files != diff_files_original:
-        try:
-            get_logger().info(f"Filtered out {len(diff_files_original) - len(diff_files)} files")
-            new_names = set([a.filename for a in diff_files])
-            orig_names = set([a.filename for a in diff_files_original])
-            get_logger().info(f"Filtered out files: {orig_names - new_names}")
-        except Exception as e:
-            pass
-
-
     # get pr languages
     pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
     if pr_languages:
@@ -155,21 +145,11 @@ def get_pr_diff(git_provider: GitProvider, token_handler: TokenHandler,
 def get_pr_diff_multiple_patchs(git_provider: GitProvider, token_handler: TokenHandler, model: str,
                 add_line_numbers_to_hunks: bool = False, disable_extra_lines: bool = False):
     try:
-        diff_files_original = git_provider.get_diff_files()
+        diff_files = git_provider.get_diff_files()
     except RateLimitExceededException as e:
         get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
 
-    diff_files = filter_ignored(diff_files_original)
-    if diff_files != diff_files_original:
-        try:
-            get_logger().info(f"Filtered out {len(diff_files_original) - len(diff_files)} files")
-            new_names = set([a.filename for a in diff_files])
-            orig_names = set([a.filename for a in diff_files_original])
-            get_logger().info(f"Filtered out files: {orig_names - new_names}")
-        except Exception as e:
-            pass
-
     # get pr languages
     pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
     if pr_languages:
@@ -195,23 +175,27 @@ def pr_generate_extended_diff(pr_languages: list,
     for lang in pr_languages:
         for file in lang['files']:
             original_file_content_str = file.base_file
+            new_file_content_str = file.head_file
             patch = file.patch
             if not patch:
                 continue
 
             # extend each patch with extra lines of context
             extended_patch = extend_patch(original_file_content_str, patch,
-                                          patch_extra_lines_before, patch_extra_lines_after, file.filename)
+                                          patch_extra_lines_before, patch_extra_lines_after, file.filename,
+                                          new_file_str=new_file_content_str)
             if not extended_patch:
                 get_logger().warning(f"Failed to extend patch for file: {file.filename}")
                 continue
-            full_extended_patch = f"\n\n## {file.filename}\n{extended_patch.rstrip()}\n"
 
             if add_line_numbers_to_hunks:
-                full_extended_patch = convert_to_hunks_with_lines_numbers(extended_patch, file)
+                full_extended_patch = decouple_and_convert_to_hunks_with_lines_numbers(extended_patch, file)
+            else:
+                extended_patch = extended_patch.replace('\n@@ ', '\n\n@@ ') # add extra line before each hunk
+                full_extended_patch = f"\n\n## File: '{file.filename.strip()}'\n\n{extended_patch.strip()}\n"
 
             # add AI-summary metadata to the patch
-            if file.ai_file_summary and  get_settings().get("config.enable_ai_metadata", False):
+            if file.ai_file_summary and get_settings().get("config.enable_ai_metadata", False):
                 full_extended_patch = add_ai_summary_top_patch(file, full_extended_patch)
 
             patch_tokens = token_handler.count_tokens(full_extended_patch)
@@ -251,7 +235,7 @@ def pr_generate_compressed_diff(top_langs: list, token_handler: TokenHandler, mo
             continue
 
         if convert_hunks_to_line_numbers:
-            patch = convert_to_hunks_with_lines_numbers(patch, file)
+            patch = decouple_and_convert_to_hunks_with_lines_numbers(patch, file)
 
         ## add AI-summary metadata to the patch (disabled, since we are in the compressed diff)
         # if file.ai_file_summary and get_settings().config.get('config.is_auto_command', False):
@@ -316,13 +300,13 @@ def generate_full_patch(convert_hunks_to_line_numbers, file_dict, max_tokens_mod
             # TODO: Option for alternative logic to remove hunks from the patch to reduce the number of tokens
             #  until we meet the requirements
             if get_settings().config.verbosity_level >= 2:
-                get_logger().warning(f"Patch too large, skipping it, {filename}")
+                get_logger().warning(f"Patch too large, skipping it: '{filename}'")
             remaining_files_list_new.append(filename)
             continue
 
         if patch:
             if not convert_hunks_to_line_numbers:
-                patch_final = f"\n\n## File: '{filename.strip()}\n\n{patch.strip()}\n'"
+                patch_final = f"\n\n## File: '{filename.strip()}'\n\n{patch.strip()}\n"
             else:
                 patch_final = "\n\n" + patch.strip()
             patches.append(patch_final)
@@ -383,7 +367,8 @@ def _get_all_deployments(all_models: List[str]) -> List[str]:
 def get_pr_multi_diffs(git_provider: GitProvider,
                        token_handler: TokenHandler,
                        model: str,
-                       max_calls: int = 5) -> List[str]:
+                       max_calls: int = 5,
+                       add_line_numbers: bool = True) -> List[str]:
     """
     Retrieves the diff files from a Git provider, sorts them by main language, and generates patches for each file.
     The patches are split into multiple groups based on the maximum number of tokens allowed for the given model.
@@ -406,8 +391,6 @@ def get_pr_multi_diffs(git_provider: GitProvider,
         get_logger().error(f"Rate limit exceeded for git provider API. original message {e}")
         raise
 
-    diff_files = filter_ignored(diff_files)
-
     # Sort files by main language
     pr_languages = sort_files_by_main_languages(git_provider.get_languages(), diff_files)
 
@@ -424,7 +407,8 @@ def get_pr_multi_diffs(git_provider: GitProvider,
 
     # try first a single run with standard diff string, with patch extension, and no deletions
     patches_extended, total_tokens, patches_extended_tokens = pr_generate_extended_diff(
-        pr_languages, token_handler, add_line_numbers_to_hunks=True,
+        pr_languages, token_handler,
+        add_line_numbers_to_hunks=add_line_numbers,
         patch_extra_lines_before=PATCH_EXTRA_LINES_BEFORE,
         patch_extra_lines_after=PATCH_EXTRA_LINES_AFTER)
 
@@ -453,7 +437,12 @@ def get_pr_multi_diffs(git_provider: GitProvider,
         if patch is None:
             continue
 
-        patch = convert_to_hunks_with_lines_numbers(patch, file)
+        # Add line numbers and metadata to the patch
+        if add_line_numbers:
+            patch = decouple_and_convert_to_hunks_with_lines_numbers(patch, file)
+        else:
+            patch = f"\n\n## File: '{file.filename.strip()}'\n\n{patch.strip()}\n"
+
         # add AI-summary metadata to the patch
         if file.ai_file_summary and get_settings().get("config.enable_ai_metadata", False):
             patch = add_ai_summary_top_patch(file, patch)
@@ -501,7 +490,7 @@ def get_pr_multi_diffs(git_provider: GitProvider,
     # Add the last chunk
     if patches:
         final_diff = "\n".join(patches)
-        final_diff_list.append(final_diff)
+        final_diff_list.append(final_diff.strip())
 
     return final_diff_list
 

pr_agent/algo/token_handler.py

@@ -19,8 +19,11 @@ class TokenEncoder:
             with cls._lock:  # Lock acquisition to ensure thread safety
                 if cls._encoder_instance is None or model != cls._model:
                     cls._model = model
-                    cls._encoder_instance = encoding_for_model(cls._model) if "gpt" in cls._model else get_encoding(
-                        "cl100k_base")
+                    try:
+                        cls._encoder_instance = encoding_for_model(cls._model) if "gpt" in cls._model else get_encoding(
+                            "o200k_base")
+                    except:
+                        cls._encoder_instance = get_encoding("o200k_base")
         return cls._encoder_instance
 
 
@@ -76,7 +79,48 @@ class TokenHandler:
             get_logger().error(f"Error in _get_system_user_tokens: {e}")
             return 0
 
-    def count_tokens(self, patch: str) -> int:
+    def calc_claude_tokens(self, patch):
+        try:
+            import anthropic
+            from pr_agent.algo import MAX_TOKENS
+            client = anthropic.Anthropic(api_key=get_settings(use_context=False).get('anthropic.key'))
+            MaxTokens = MAX_TOKENS[get_settings().config.model]
+
+            # Check if the content size is too large (9MB limit)
+            if len(patch.encode('utf-8')) > 9_000_000:
+                get_logger().warning(
+                    "Content too large for Anthropic token counting API, falling back to local tokenizer"
+                )
+                return MaxTokens
+
+            response = client.messages.count_tokens(
+                model="claude-3-7-sonnet-20250219",
+                system="system",
+                messages=[{
+                    "role": "user",
+                    "content": patch
+                }],
+            )
+            return response.input_tokens
+
+        except Exception as e:
+            get_logger().error( f"Error in Anthropic token counting: {e}")
+            return MaxTokens
+
+    def estimate_token_count_for_non_anth_claude_models(self, model, default_encoder_estimate):
+        from math import ceil
+        import re
+
+        model_is_from_o_series = re.match(r"^o[1-9](-mini|-preview)?$", model)
+        if ('gpt' in get_settings().config.model.lower() or model_is_from_o_series) and get_settings(use_context=False).get('openai.key'):
+            return default_encoder_estimate
+        #else: Model is not an OpenAI one - therefore, cannot provide an accurate token count and instead, return a higher number as best effort.
+
+        elbow_factor = 1 + get_settings().get('config.model_token_count_estimate_factor', 0)
+        get_logger().warning(f"{model}'s expected token count cannot be accurately estimated. Using {elbow_factor} of encoder output as best effort estimate")
+        return ceil(elbow_factor * default_encoder_estimate)
+
+    def count_tokens(self, patch: str, force_accurate=False) -> int:
         """
         Counts the number of tokens in a given patch string.
 
@@ -86,4 +130,16 @@ class TokenHandler:
         Returns:
         The number of tokens in the patch string.
         """
-        return len(self.encoder.encode(patch, disallowed_special=()))
+        encoder_estimate = len(self.encoder.encode(patch, disallowed_special=()))
+
+        #If an estimate is enough (for example, in cases where the maximal allowed tokens is way below the known limits), return it.
+        if not force_accurate:
+            return encoder_estimate
+
+        #else, force_accurate==True: User requested providing an accurate estimation:
+        model = get_settings().config.model.lower()
+        if 'claude' in model and get_settings(use_context=False).get('anthropic.key'):
+            return self.calc_claude_tokens(patch) # API call to Anthropic for accurate token counting for Claude models
+
+        #else: Non Anthropic provided model:
+        return self.estimate_token_count_for_non_anth_claude_models(model, encoder_estimate)

pr_agent/algo/types.py

@@ -1,5 +1,6 @@
 from dataclasses import dataclass
 from enum import Enum
+from typing import Optional
 
 
 class EDIT_TYPE(Enum):
@@ -21,4 +22,5 @@ class FilePatchInfo:
     old_filename: str = None
     num_plus_lines: int = -1
     num_minus_lines: int = -1
+    language: Optional[str] = None
     ai_file_summary: str = None

pr_agent/algo/utils.py

@@ -23,6 +23,7 @@ from pydantic import BaseModel
 from starlette_context import context
 
 from pr_agent.algo import MAX_TOKENS
+from pr_agent.algo.git_patch_processing import extract_hunk_lines_from_patch
 from pr_agent.algo.token_handler import TokenEncoder
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.config_loader import get_settings, global_settings
@@ -49,6 +50,11 @@ class PRReviewHeader(str, Enum):
     REGULAR = "## PR Reviewer Guide"
     INCREMENTAL = "## Incremental PR Reviewer Guide"
 
+class ReasoningEffort(str, Enum):
+    HIGH = "high"
+    MEDIUM = "medium"
+    LOW = "low"
+
 
 class PRDescriptionHeader(str, Enum):
     CHANGES_WALKTHROUGH = "### **Changes walkthrough** 📝"
@@ -235,7 +241,7 @@ def convert_to_markdown_v2(output_data: dict,
                         start_line = int(str(issue.get('start_line', 0)).strip())
                         end_line = int(str(issue.get('end_line', 0)).strip())
 
-                        relevant_lines_str = extract_relevant_lines_str(end_line, files, relevant_file, start_line)
+                        relevant_lines_str = extract_relevant_lines_str(end_line, files, relevant_file, start_line, dedent=True)
                         if git_provider:
                             reference_link = git_provider.get_line_link(relevant_file, start_line, end_line)
                         else:
@@ -244,7 +250,7 @@ def convert_to_markdown_v2(output_data: dict,
                         if gfm_supported:
                             if reference_link is not None and len(reference_link) > 0:
                                 if relevant_lines_str:
-                                    issue_str = f"<details><summary><a href='{reference_link}'><strong>{issue_header}</strong></a>\n\n{issue_content}</summary>\n\n{relevant_lines_str}\n\n</details>"
+                                    issue_str = f"<details><summary><a href='{reference_link}'><strong>{issue_header}</strong></a>\n\n{issue_content}\n</summary>\n\n{relevant_lines_str}\n\n</details>"
                                 else:
                                     issue_str = f"<a href='{reference_link}'><strong>{issue_header}</strong></a><br>{issue_content}"
                             else:
@@ -270,25 +276,13 @@ def convert_to_markdown_v2(output_data: dict,
     if gfm_supported:
         markdown_text += "</table>\n"
 
-    if 'code_feedback' in output_data:
-        if gfm_supported:
-            markdown_text += f"\n\n"
-            markdown_text += f"<details><summary> <strong>Code feedback:</strong></summary>\n\n"
-            markdown_text += "<hr>"
-        else:
-            markdown_text += f"\n\n### Code feedback:\n\n"
-        for i, value in enumerate(output_data['code_feedback']):
-            if value is None or value == '' or value == {} or value == []:
-                continue
-            markdown_text += parse_code_suggestion(value, i, gfm_supported)+"\n\n"
-        if markdown_text.endswith('<hr>'):
-            markdown_text= markdown_text[:-4]
-        if gfm_supported:
-            markdown_text += f"</details>"
-
     return markdown_text
 
-def extract_relevant_lines_str(end_line, files, relevant_file, start_line):
+
+def extract_relevant_lines_str(end_line, files, relevant_file, start_line, dedent=False) -> str:
+    """
+    Finds 'relevant_file' in 'files', and extracts the lines from 'start_line' to 'end_line' string from the file content.
+    """
     try:
         relevant_lines_str = ""
         if files:
@@ -296,12 +290,29 @@ def extract_relevant_lines_str(end_line, files, relevant_file, start_line):
             for file in files:
                 if file.filename.strip() == relevant_file:
                     if not file.head_file:
-                        get_logger().warning(f"No content found in file: {file.filename}")
-                        return ""
-                    relevant_file_lines = file.head_file.splitlines()
-                    relevant_lines_str = "\n".join(relevant_file_lines[start_line - 1:end_line])
+                        # as a fallback, extract relevant lines directly from patch
+                        patch = file.patch
+                        get_logger().info(f"No content found in file: '{file.filename}' for 'extract_relevant_lines_str'. Using patch instead")
+                        _, selected_lines = extract_hunk_lines_from_patch(patch, file.filename, start_line, end_line,side='right')
+                        if not selected_lines:
+                            get_logger().error(f"Failed to extract relevant lines from patch: {file.filename}")
+                            return ""
+                        # filter out '-' lines
+                        relevant_lines_str = ""
+                        for line in selected_lines.splitlines():
+                            if line.startswith('-'):
+                                continue
+                            relevant_lines_str += line[1:] + '\n'
+                    else:
+                        relevant_file_lines = file.head_file.splitlines()
+                        relevant_lines_str = "\n".join(relevant_file_lines[start_line - 1:end_line])
+
+                    if dedent and relevant_lines_str:
+                        # Remove the longest leading string of spaces and tabs common to all lines.
+                        relevant_lines_str = textwrap.dedent(relevant_lines_str)
                     relevant_lines_str = f"```{file.language}\n{relevant_lines_str}\n```"
                     break
+
         return relevant_lines_str
     except Exception as e:
         get_logger().exception(f"Failed to extract relevant lines: {e}")
@@ -310,47 +321,98 @@ def extract_relevant_lines_str(end_line, files, relevant_file, start_line):
 
 def ticket_markdown_logic(emoji, markdown_text, value, gfm_supported) -> str:
     ticket_compliance_str = ""
-    final_compliance_level = -1
+    compliance_emoji = ''
+    # Track compliance levels across all tickets
+    all_compliance_levels = []
+
     if isinstance(value, list):
-        for v in value:
-            ticket_url = v.get('ticket_url', '').strip()
-            compliance_level = v.get('overall_compliance_level', '').strip()
-            # add emojis, if 'Fully compliant' ✅, 'Partially compliant' 🔶, or 'Not compliant' ❌
-            if compliance_level.lower() == 'fully compliant':
-                # compliance_level = '✅ Fully compliant'
-                final_compliance_level = 2 if final_compliance_level == -1 else 1
-            elif compliance_level.lower() == 'partially compliant':
-                # compliance_level = '🔶 Partially compliant'
-                final_compliance_level = 1
-            elif compliance_level.lower() == 'not compliant':
-                # compliance_level = '❌ Not compliant'
-                final_compliance_level = 0 if final_compliance_level < 1 else 1
+        for ticket_analysis in value:
+            try:
+                ticket_url = ticket_analysis.get('ticket_url', '').strip()
+                explanation = ''
+                ticket_compliance_level = ''  # Individual ticket compliance
+                fully_compliant_str = ticket_analysis.get('fully_compliant_requirements', '').strip()
+                not_compliant_str = ticket_analysis.get('not_compliant_requirements', '').strip()
+                requires_further_human_verification = ticket_analysis.get('requires_further_human_verification',
+                                                                          '').strip()
 
-            # explanation = v.get('compliance_analysis', '').strip()
-            explanation = ''
-            fully_compliant_str = v.get('fully_compliant_requirements', '').strip()
-            not_compliant_str = v.get('not_compliant_requirements', '').strip()
-            if fully_compliant_str:
-                explanation += f"Fully compliant requirements:\n{fully_compliant_str}\n\n"
-            if not_compliant_str:
-                explanation += f"Not compliant requirements:\n{not_compliant_str}\n\n"
+                if not fully_compliant_str and not not_compliant_str:
+                    get_logger().debug(f"Ticket compliance has no requirements",
+                                       artifact={'ticket_url': ticket_url})
+                    continue
 
-            ticket_compliance_str += f"\n\n**[{ticket_url.split('/')[-1]}]({ticket_url}) - {compliance_level}**\n\n{explanation}\n\n"
-        if final_compliance_level == 2:
-            compliance_level = '✅'
-        elif final_compliance_level == 1:
-            compliance_level = '🔶'
-        else:
-            compliance_level = '❌'
+                # Calculate individual ticket compliance level
+                if fully_compliant_str:
+                    if not_compliant_str:
+                        ticket_compliance_level = 'Partially compliant'
+                    else:
+                        if not requires_further_human_verification:
+                            ticket_compliance_level = 'Fully compliant'
+                        else:
+                            ticket_compliance_level = 'PR Code Verified'
+                elif not_compliant_str:
+                    ticket_compliance_level = 'Not compliant'
 
+                # Store the compliance level for aggregation
+                if ticket_compliance_level:
+                    all_compliance_levels.append(ticket_compliance_level)
+
+                # build compliance string
+                if fully_compliant_str:
+                    explanation += f"Compliant requirements:\n\n{fully_compliant_str}\n\n"
+                if not_compliant_str:
+                    explanation += f"Non-compliant requirements:\n\n{not_compliant_str}\n\n"
+                if requires_further_human_verification:
+                    explanation += f"Requires further human verification:\n\n{requires_further_human_verification}\n\n"
+                ticket_compliance_str += f"\n\n**[{ticket_url.split('/')[-1]}]({ticket_url}) - {ticket_compliance_level}**\n\n{explanation}\n\n"
+
+                # for debugging
+                if requires_further_human_verification:
+                    get_logger().debug(f"Ticket compliance requires further human verification",
+                                       artifact={'ticket_url': ticket_url,
+                                                 'requires_further_human_verification': requires_further_human_verification,
+                                                 'compliance_level': ticket_compliance_level})
+
+            except Exception as e:
+                get_logger().exception(f"Failed to process ticket compliance: {e}")
+                continue
+
+        # Calculate overall compliance level and emoji
+        if all_compliance_levels:
+            if all(level == 'Fully compliant' for level in all_compliance_levels):
+                compliance_level = 'Fully compliant'
+                compliance_emoji = '✅'
+            elif all(level == 'PR Code Verified' for level in all_compliance_levels):
+                compliance_level = 'PR Code Verified'
+                compliance_emoji = '✅'
+            elif any(level == 'Not compliant' for level in all_compliance_levels):
+                # If there's a mix of compliant and non-compliant tickets
+                if any(level in ['Fully compliant', 'PR Code Verified'] for level in all_compliance_levels):
+                    compliance_level = 'Partially compliant'
+                    compliance_emoji = '🔶'
+                else:
+                    compliance_level = 'Not compliant'
+                    compliance_emoji = '❌'
+            elif any(level == 'Partially compliant' for level in all_compliance_levels):
+                compliance_level = 'Partially compliant'
+                compliance_emoji = '🔶'
+            else:
+                compliance_level = 'PR Code Verified'
+                compliance_emoji = '✅'
+
+            # Set extra statistics outside the ticket loop
+            get_settings().set('config.extra_statistics', {'compliance_level': compliance_level})
+
+        # editing table row for ticket compliance analysis
         if gfm_supported:
             markdown_text += f"<tr><td>\n\n"
-            markdown_text += f"**{emoji} Ticket compliance analysis {compliance_level}**\n\n"
+            markdown_text += f"**{emoji} Ticket compliance analysis {compliance_emoji}**\n\n"
             markdown_text += ticket_compliance_str
             markdown_text += f"</td></tr>\n"
         else:
-            markdown_text += f"### {emoji} Ticket compliance analysis {compliance_level}\n\n"
-            markdown_text += ticket_compliance_str+"\n\n"
+            markdown_text += f"### {emoji} Ticket compliance analysis {compliance_emoji}\n\n"
+            markdown_text += ticket_compliance_str + "\n\n"
+
     return markdown_text
 
 
@@ -577,27 +639,22 @@ def load_large_diff(filename, new_file_content_str: str, original_file_content_s
     """
     Generate a patch for a modified file by comparing the original content of the file with the new content provided as
     input.
-
-    Args:
-        new_file_content_str: The new content of the file as a string.
-        original_file_content_str: The original content of the file as a string.
-
-    Returns:
-        The generated or provided patch string.
-
-    Raises:
-        None.
     """
-    patch = ""
+    if not original_file_content_str and not new_file_content_str:
+        return ""
+
     try:
+        original_file_content_str = (original_file_content_str or "").rstrip() + "\n"
+        new_file_content_str = (new_file_content_str or "").rstrip() + "\n"
         diff = difflib.unified_diff(original_file_content_str.splitlines(keepends=True),
                                     new_file_content_str.splitlines(keepends=True))
         if get_settings().config.verbosity_level >= 2 and show_warning:
-            get_logger().warning(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
+            get_logger().info(f"File was modified, but no patch was found. Manually creating patch: {filename}.")
         patch = ''.join(diff)
-    except Exception:
-        pass
-    return patch
+        return patch
+    except Exception as e:
+        get_logger().exception(f"Failed to generate patch for file: {filename}")
+        return ""
 
 
 def update_settings_from_args(args: List[str]) -> List[str]:
@@ -647,12 +704,14 @@ def _fix_key_value(key: str, value: str):
 
 
 def load_yaml(response_text: str, keys_fix_yaml: List[str] = [], first_key="", last_key="") -> dict:
+    response_text_original = copy.deepcopy(response_text)
     response_text = response_text.strip('\n').removeprefix('```yaml').rstrip().removesuffix('```')
     try:
         data = yaml.safe_load(response_text)
     except Exception as e:
         get_logger().warning(f"Initial failure to parse AI prediction: {e}")
-        data = try_fix_yaml(response_text, keys_fix_yaml=keys_fix_yaml, first_key=first_key, last_key=last_key)
+        data = try_fix_yaml(response_text, keys_fix_yaml=keys_fix_yaml, first_key=first_key, last_key=last_key,
+                            response_text_original=response_text_original)
         if not data:
             get_logger().error(f"Failed to parse AI prediction after fallbacks",
                                artifact={'response_text': response_text})
@@ -666,7 +725,8 @@ def load_yaml(response_text: str, keys_fix_yaml: List[str] = [], first_key="", l
 def try_fix_yaml(response_text: str,
                  keys_fix_yaml: List[str] = [],
                  first_key="",
-                 last_key="",) -> dict:
+                 last_key="",
+                 response_text_original="") -> dict:
     response_text_lines = response_text.split('\n')
 
     keys_yaml = ['relevant line:', 'suggestion content:', 'relevant file:', 'existing code:', 'improved code:']
@@ -683,11 +743,13 @@ def try_fix_yaml(response_text: str,
         get_logger().info(f"Successfully parsed AI prediction after adding |-\n")
         return data
     except:
-        get_logger().info(f"Failed to parse AI prediction after adding |-\n")
+        pass
 
     # second fallback - try to extract only range from first ```yaml to ````
     snippet_pattern = r'```(yaml)?[\s\S]*?```'
     snippet = re.search(snippet_pattern, '\n'.join(response_text_lines_copy))
+    if not snippet:
+        snippet = re.search(snippet_pattern, response_text_original) # before we removed the "```"
     if snippet:
         snippet_text = snippet.group()
         try:
@@ -727,9 +789,19 @@ def try_fix_yaml(response_text: str,
         except:
             pass
 
+    # fifth fallback - try to remove leading '+' (sometimes added by AI for 'existing code' and 'improved code')
+    response_text_lines_copy = response_text_lines.copy()
+    for i in range(0, len(response_text_lines_copy)):
+        if response_text_lines_copy[i].startswith('+'):
+            response_text_lines_copy[i] = ' ' + response_text_lines_copy[i][1:]
+    try:
+        data = yaml.safe_load('\n'.join(response_text_lines_copy))
+        get_logger().info(f"Successfully parsed AI prediction after removing leading '+'")
+        return data
+    except:
+        pass
 
-    # fifth fallback - try to remove last lines
-    data = {}
+    # sixth fallback - try to remove last lines
     for i in range(1, len(response_text_lines)):
         response_text_lines_tmp = '\n'.join(response_text_lines[:-i])
         try:

pr_agent/cli.py

@@ -22,6 +22,7 @@ def set_parser():
     - cli.py --pr_url=... ask "write me a poem about this PR"
     - cli.py --pr_url=... reflect
     - cli.py --issue_url=... similar_issue
+    - cli.py --pr_url/--issue_url= help_docs [<asked question>]
 
     Supported commands:
     - review / review_pr - Add a review that includes a summary of the PR and specific suggestions for improvement.
@@ -40,6 +41,8 @@ def set_parser():
     - add_docs
 
     - generate_labels
+    
+    - help_docs - Ask a question, from either an issue or PR context, on a given repo (current context or a different one)
 
 
     Configuration:

pr_agent/config_loader.py

@@ -12,7 +12,6 @@ global_settings = Dynaconf(
     envvar_prefix=False,
     merge_enabled=True,
     settings_files=[join(current_dir, f) for f in [
-        "settings/.secrets.toml",
         "settings/configuration.toml",
         "settings/ignore.toml",
         "settings/language_extensions.toml",
@@ -20,21 +19,24 @@ global_settings = Dynaconf(
         "settings/pr_questions_prompts.toml",
         "settings/pr_line_questions_prompts.toml",
         "settings/pr_description_prompts.toml",
-        "settings/pr_code_suggestions_prompts.toml",
-        "settings/pr_code_suggestions_reflect_prompts.toml",
-        "settings/pr_sort_code_suggestions_prompts.toml",
+        "settings/code_suggestions/pr_code_suggestions_prompts.toml",
+        "settings/code_suggestions/pr_code_suggestions_prompts_not_decoupled.toml",
+        "settings/code_suggestions/pr_code_suggestions_reflect_prompts.toml",
         "settings/pr_information_from_user_prompts.toml",
         "settings/pr_update_changelog_prompts.toml",
         "settings/pr_custom_labels.toml",
         "settings/pr_add_docs.toml",
         "settings/custom_labels.toml",
         "settings/pr_help_prompts.toml",
+        "settings/pr_help_docs_prompts.toml",
+        "settings/pr_help_docs_headings_prompts.toml",
+        "settings/.secrets.toml",
         "settings_prod/.secrets.toml",
     ]]
 )
 
 
-def get_settings():
+def get_settings(use_context=False):
     """
     Retrieves the current settings.
 

pr_agent/git_providers/azuredevops_provider.py

@@ -183,6 +183,7 @@ class AzureDevopsProvider(GitProvider):
         return True
 
     def set_pr(self, pr_url: str):
+        self.pr_url = pr_url
         self.workspace_slug, self.repo_slug, self.pr_num = self._parse_pr_url(pr_url)
         self.pr = self._get_pr()
 
@@ -326,13 +327,13 @@ class AzureDevopsProvider(GitProvider):
                     edit_type = EDIT_TYPE.ADDED
                 elif diff_types[file] == "delete":
                     edit_type = EDIT_TYPE.DELETED
-                elif diff_types[file] == "rename":
+                elif "rename" in diff_types[file]: # diff_type can be `rename` | `edit, rename`
                     edit_type = EDIT_TYPE.RENAMED
 
                 version = GitVersionDescriptor(
                     version=base_sha.commit_id, version_type="commit"
                 )
-                if edit_type == EDIT_TYPE.ADDED:
+                if edit_type == EDIT_TYPE.ADDED or edit_type == EDIT_TYPE.RENAMED:
                     original_file_content_str = ""
                 else:
                     try:
@@ -382,7 +383,7 @@ class AzureDevopsProvider(GitProvider):
             get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return None
         comment = Comment(content=pr_comment)
-        thread = CommentThread(comments=[comment], thread_context=thread_context, status=5)
+        thread = CommentThread(comments=[comment], thread_context=thread_context, status=1)
         thread_response = self.azure_devops_client.create_thread(
             comment_thread=thread,
             project=self.workspace_slug,
@@ -614,8 +615,11 @@ class AzureDevopsProvider(GitProvider):
             return pr_id
         except Exception as e:
             if get_settings().config.verbosity_level >= 2:
-                get_logger().error(f"Failed to get pr id, error: {e}")
+                get_logger().info(f"Failed to get pr id, error: {e}")
             return ""
 
     def publish_file_comments(self, file_comments: list) -> bool:
         pass
+
+    def get_line_link(self, relevant_file: str, relevant_line_start: int, relevant_line_end: int = None) -> str:
+        return self.pr_url+f"?_a=files&path={relevant_file}"

pr_agent/git_providers/bitbucket_provider.py

@@ -29,14 +29,36 @@ class BitbucketProvider(GitProvider):
         self, pr_url: Optional[str] = None, incremental: Optional[bool] = False
     ):
         s = requests.Session()
-        try:
-            bearer = context.get("bitbucket_bearer_token", None)
-            s.headers["Authorization"] = f"Bearer {bearer}"
-        except Exception:
-            s.headers[
-                "Authorization"
-            ] = f'Bearer {get_settings().get("BITBUCKET.BEARER_TOKEN", None)}'
         s.headers["Content-Type"] = "application/json"
+
+        self.auth_type = get_settings().get("BITBUCKET.AUTH_TYPE", "bearer")
+
+        try:
+            def get_token(token_name, auth_type_name):
+                token = get_settings().get(f"BITBUCKET.{token_name.upper()}", None)
+                if not token:
+                    raise ValueError(f"{auth_type_name} auth requires a token")
+                return token
+
+            if self.auth_type == "basic":
+                self.basic_token = get_token("basic_token", "Basic")
+                s.headers["Authorization"] = f"Basic {self.basic_token}"
+            elif self.auth_type == "bearer":
+                try:
+                    self.bearer_token = context.get("bitbucket_bearer_token", None)
+                except:
+                    self.bearer_token = None
+
+                if not self.bearer_token:
+                    self.bearer_token = get_token("bearer_token", "Bearer")
+                s.headers["Authorization"] = f"Bearer {self.bearer_token}"
+            else:
+                 raise ValueError(f"Unsupported auth_type: {self.auth_type}")
+
+        except Exception as e:
+            get_logger().exception(f"Failed to initialize Bitbucket authentication: {e}")
+            raise
+
         self.headers = s.headers
         self.bitbucket_client = Cloud(session=s)
         self.max_comment_length = 31000
@@ -67,6 +89,37 @@ class BitbucketProvider(GitProvider):
         except Exception:
             return ""
 
+    def get_git_repo_url(self, pr_url: str=None) -> str: #bitbucket does not support issue url, so ignore param
+        try:
+            parsed_url = urlparse(self.pr_url)
+            return f"{parsed_url.scheme}://{parsed_url.netloc}/{self.workspace_slug}/{self.repo_slug}.git"
+        except Exception as e:
+            get_logger().exception(f"url is not a valid merge requests url: {self.pr_url}")
+            return ""
+
+    # Given a git repo url, return prefix and suffix of the provider in order to view a given file belonging to that repo.
+    # Example: git clone git clone https://bitbucket.org/codiumai/pr-agent.git and branch: main -> prefix: "https://bitbucket.org/codiumai/pr-agent/src/main", suffix: ""
+    # In case git url is not provided, provider will use PR context (which includes branch) to determine the prefix and suffix.
+    def get_canonical_url_parts(self, repo_git_url:str=None, desired_branch:str=None) -> Tuple[str, str]:
+        scheme_and_netloc = None
+        if repo_git_url:
+            parsed_git_url = urlparse(repo_git_url)
+            scheme_and_netloc = parsed_git_url.scheme + "://" + parsed_git_url.netloc
+            repo_path = parsed_git_url.path.split('.git')[0][1:] #/<workspace>/<repo>.git -> <workspace>/<repo>
+            if repo_path.count('/') != 1:
+                get_logger().error(f"repo_git_url is not a valid git repo url: {repo_git_url}")
+                return ("", "")
+            workspace_name, project_name = repo_path.split('/')
+        else:
+            desired_branch = self.get_repo_default_branch()
+            parsed_pr_url = urlparse(self.pr_url)
+            scheme_and_netloc = parsed_pr_url.scheme + "://" + parsed_pr_url.netloc
+            workspace_name, project_name = (self.workspace_slug, self.repo_slug)
+        prefix = f"{scheme_and_netloc}/{workspace_name}/{project_name}/src/{desired_branch}"
+        suffix = "" #None
+        return (prefix, suffix)
+
+
     def publish_code_suggestions(self, code_suggestions: list) -> bool:
         """
         Publishes code suggestions as comments on the PR.
@@ -436,6 +489,16 @@ class BitbucketProvider(GitProvider):
     def get_pr_branch(self):
         return self.pr.source_branch
 
+    # This function attempts to get the default branch of the repository. As a fallback, uses the PR destination branch.
+    # Note: Must be running from a PR context.
+    def get_repo_default_branch(self):
+        try:
+            url_repo = f"https://api.bitbucket.org/2.0/repositories/{self.workspace_slug}/{self.repo_slug}/"
+            response_repo = requests.request("GET", url_repo, headers=self.headers).json()
+            return response_repo['mainbranch']['name']
+        except:
+            return self.pr.destination_branch
+
     def get_pr_owner_id(self) -> str | None:
         return self.workspace_slug
 
@@ -457,7 +520,7 @@ class BitbucketProvider(GitProvider):
         return True
 
     @staticmethod
-    def _parse_pr_url(pr_url: str) -> Tuple[str, int]:
+    def _parse_pr_url(pr_url: str) -> Tuple[str, int, int]:
         parsed_url = urlparse(pr_url)
 
         if "bitbucket.org" not in parsed_url.netloc:
@@ -559,3 +622,26 @@ class BitbucketProvider(GitProvider):
     # bitbucket does not support labels
     def get_pr_labels(self, update=False):
         pass
+    #Clone related
+    def _prepare_clone_url_with_token(self, repo_url_to_clone: str) -> str | None:
+        if "bitbucket.org" not in repo_url_to_clone:
+            get_logger().error("Repo URL is not a valid bitbucket URL.")
+            return None
+
+        (scheme, base_url) = repo_url_to_clone.split("bitbucket.org")
+        if not all([scheme, base_url]):
+            get_logger().error(f"repo_url_to_clone: {repo_url_to_clone} is not a valid bitbucket URL.")
+            return None
+
+        if self.auth_type == "basic":
+            # Basic auth with token
+            clone_url = f"{scheme}x-token-auth:{self.basic_token}@bitbucket.org{base_url}"
+        elif self.auth_type == "bearer":
+            # Bearer token
+            clone_url = f"{scheme}x-token-auth:{self.bearer_token}@bitbucket.org{base_url}"
+        else:
+            # This case should ideally not be reached if __init__ validates auth_type
+            get_logger().error(f"Unsupported or uninitialized auth_type: {getattr(self, 'auth_type', 'N/A')}. Returning None")
+            return None
+
+        return clone_url

pr_agent/git_providers/bitbucket_server_provider.py

@@ -7,6 +7,8 @@ from urllib.parse import quote_plus, urlparse
 
 from atlassian.bitbucket import Bitbucket
 from requests.exceptions import HTTPError
+import shlex
+import subprocess
 
 from ..algo.git_patch_processing import decode_if_bytes
 from ..algo.language_handler import is_valid_file
@@ -34,7 +36,7 @@ class BitbucketServerProvider(GitProvider):
         self.incremental = incremental
         self.diff_files = None
         self.bitbucket_pull_request_api_url = pr_url
-
+        self.bearer_token = get_settings().get("BITBUCKET_SERVER.BEARER_TOKEN", None)
         self.bitbucket_server_url = self._parse_bitbucket_server(url=pr_url)
         self.bitbucket_client = bitbucket_client or Bitbucket(url=self.bitbucket_server_url,
                                                               token=get_settings().get("BITBUCKET_SERVER.BEARER_TOKEN",
@@ -47,6 +49,41 @@ class BitbucketServerProvider(GitProvider):
         if pr_url:
             self.set_pr(pr_url)
 
+    def get_git_repo_url(self, pr_url: str=None) -> str: #bitbucket server does not support issue url, so ignore param
+        try:
+            parsed_url = urlparse(self.pr_url)
+            return f"{parsed_url.scheme}://{parsed_url.netloc}/scm/{self.workspace_slug.lower()}/{self.repo_slug.lower()}.git"
+        except Exception as e:
+            get_logger().exception(f"url is not a valid merge requests url: {self.pr_url}")
+            return ""
+
+    # Given a git repo url, return prefix and suffix of the provider in order to view a given file belonging to that repo.
+    # Example: https://bitbucket.dev.my_inc.com/scm/my_work/my_repo.git and branch: my_branch -> prefix: "https://bitbucket.dev.my_inc.com/projects/MY_WORK/repos/my_repo/browse/src", suffix: "?at=refs%2Fheads%2Fmy_branch"
+    # In case git url is not provided, provider will use PR context (which includes branch) to determine the prefix and suffix.
+    def get_canonical_url_parts(self, repo_git_url:str=None, desired_branch:str=None) -> Tuple[str, str]:
+        workspace_name = None
+        project_name = None
+        if not repo_git_url:
+            workspace_name = self.workspace_slug
+            project_name = self.repo_slug
+            default_branch_dict = self.bitbucket_client.get_default_branch(workspace_name, project_name)
+            if 'displayId' in default_branch_dict:
+                desired_branch = default_branch_dict['displayId']
+            else:
+                get_logger().error(f"Cannot obtain default branch for workspace_name={workspace_name}, "
+                                   f"project_name={project_name}, default_branch_dict={default_branch_dict}")
+                return ("", "")
+        elif '.git' in repo_git_url and 'scm/' in repo_git_url:
+            repo_path = repo_git_url.split('.git')[0].split('scm/')[-1]
+            if repo_path.count('/') == 1:  # Has to have the form <workspace>/<repo>
+                workspace_name, project_name = repo_path.split('/')
+        if not workspace_name or not project_name:
+            get_logger().error(f"workspace_name or project_name not found in context, either git url: {repo_git_url} or uninitialized workspace/project.")
+            return ("", "")
+        prefix = f"{self.bitbucket_server_url}/projects/{workspace_name}/repos/{project_name}/browse"
+        suffix = f"?at=refs%2Fheads%2F{desired_branch}"
+        return (prefix, suffix)
+
     def get_repo_settings(self):
         try:
             content = self.bitbucket_client.get_content_of_file(self.workspace_slug, self.repo_slug, ".pr_agent.toml", self.get_pr_branch())
@@ -234,7 +271,7 @@ class BitbucketServerProvider(GitProvider):
                     new_file_content_str = self.get_file(file_path, head_sha)
                     new_file_content_str = decode_if_bytes(new_file_content_str)
 
-            patch = load_large_diff(file_path, new_file_content_str, original_file_content_str)
+            patch = load_large_diff(file_path, new_file_content_str, original_file_content_str, show_warning=False)
 
             diff_files.append(
                 FilePatchInfo(
@@ -402,10 +439,21 @@ class BitbucketServerProvider(GitProvider):
 
         try:
             projects_index = path_parts.index("projects")
-        except ValueError as e:
+        except ValueError:
+            projects_index = -1
+
+        try:
+            users_index = path_parts.index("users")
+        except ValueError:
+            users_index = -1
+
+        if projects_index == -1 and users_index == -1:
             raise ValueError(f"The provided URL '{pr_url}' does not appear to be a Bitbucket PR URL")
 
-        path_parts = path_parts[projects_index:]
+        if projects_index != -1:
+            path_parts = path_parts[projects_index:]
+        else:
+            path_parts = path_parts[users_index:]
 
         if len(path_parts) < 6 or path_parts[2] != "repos" or path_parts[4] != "pull-requests":
             raise ValueError(
@@ -413,6 +461,8 @@ class BitbucketServerProvider(GitProvider):
             )
 
         workspace_slug = path_parts[1]
+        if users_index != -1:
+            workspace_slug = f"~{workspace_slug}"
         repo_slug = path_parts[3]
         try:
             pr_number = int(path_parts[5])
@@ -468,3 +518,28 @@ class BitbucketServerProvider(GitProvider):
 
     def _get_merge_base(self):
         return f"rest/api/latest/projects/{self.workspace_slug}/repos/{self.repo_slug}/pull-requests/{self.pr_num}/merge-base"
+    # Clone related
+    def _prepare_clone_url_with_token(self, repo_url_to_clone: str) -> str | None:
+        if 'bitbucket.' not in repo_url_to_clone:
+            get_logger().error("Repo URL is not a valid bitbucket URL.")
+            return None
+        bearer_token = self.bearer_token
+        if not bearer_token:
+            get_logger().error("No bearer token provided. Returning None")
+            return None
+        # Return unmodified URL as the token is passed via HTTP headers in _clone_inner, as seen below.
+        return repo_url_to_clone
+
+    #Overriding the shell command, since for some reason usage of x-token-auth doesn't work, as mentioned here:
+    # https://stackoverflow.com/questions/56760396/cloning-bitbucket-server-repo-with-access-tokens
+    def _clone_inner(self, repo_url: str, dest_folder: str, operation_timeout_in_seconds: int=None):
+        bearer_token = self.bearer_token
+        if not bearer_token:
+            #Shouldn't happen since this is checked in _prepare_clone, therefore - throwing an exception.
+            raise RuntimeError(f"Bearer token is required!")
+
+        cli_args = shlex.split(f"git clone -c http.extraHeader='Authorization: Bearer {bearer_token}' "
+                               f"--filter=blob:none --depth 1 {repo_url} {dest_folder}")
+
+        subprocess.run(cli_args, check=True,  # check=True will raise an exception if the command fails
+            stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, timeout=operation_timeout_in_seconds)

pr_agent/git_providers/git_provider.py

@@ -1,6 +1,9 @@
 from abc import ABC, abstractmethod
 # enum EDIT_TYPE (ADDED, DELETED, MODIFIED, RENAMED)
-from typing import Optional
+import os
+import shutil
+import subprocess
+from typing import Optional, Tuple
 
 from pr_agent.algo.types import FilePatchInfo
 from pr_agent.algo.utils import Range, process_description
@@ -14,6 +17,75 @@ class GitProvider(ABC):
     def is_supported(self, capability: str) -> bool:
         pass
 
+    #Given a url (issues or PR/MR) - get the .git repo url to which they belong. Needs to be implemented by the provider.
+    def get_git_repo_url(self, issues_or_pr_url: str) -> str:
+        get_logger().warning("Not implemented! Returning empty url")
+        return ""
+
+    # Given a git repo url, return prefix and suffix of the provider in order to view a given file belonging to that repo. Needs to be implemented by the provider.
+    # For example: For a git: https://git_provider.com/MY_PROJECT/MY_REPO.git and desired branch: <MY_BRANCH> then it should return ('https://git_provider.com/projects/MY_PROJECT/repos/MY_REPO/.../<MY_BRANCH>', '?=<SOME HEADER>')
+    # so that to properly view the file: docs/readme.md -> <PREFIX>/docs/readme.md<SUFFIX> -> https://git_provider.com/projects/MY_PROJECT/repos/MY_REPO/<MY_BRANCH>/docs/readme.md?=<SOME HEADER>)
+    def get_canonical_url_parts(self, repo_git_url:str, desired_branch:str) -> Tuple[str, str]:
+        get_logger().warning("Not implemented! Returning empty prefix and suffix")
+        return ("", "")
+
+
+    #Clone related API
+    #An object which ensures deletion of a cloned repo, once it becomes out of scope.
+    # Example usage:
+    #    with TemporaryDirectory() as tmp_dir:
+    #            returned_obj: GitProvider.ScopedClonedRepo = self.git_provider.clone(self.repo_url, tmp_dir, remove_dest_folder=False)
+    #            print(returned_obj.path) #Use returned_obj.path.
+    #    #From this point, returned_obj.path may be deleted at any point and therefore must not be used.
+    class ScopedClonedRepo(object):
+        def __init__(self, dest_folder):
+            self.path = dest_folder
+
+        def __del__(self):
+            if self.path and os.path.exists(self.path):
+                shutil.rmtree(self.path, ignore_errors=True)
+
+    #Method to allow implementors to manipulate the repo url to clone (such as embedding tokens in the url string). Needs to be implemented by the provider.
+    def _prepare_clone_url_with_token(self, repo_url_to_clone: str) -> str | None:
+        get_logger().warning("Not implemented! Returning None")
+        return None
+
+    # Does a shallow clone, using a forked process to support a timeout guard.
+    # In case operation has failed, it is expected to throw an exception as this method does not return a value.
+    def _clone_inner(self, repo_url: str, dest_folder: str, operation_timeout_in_seconds: int=None) -> None:
+        #The following ought to be equivalent to:
+        # #Repo.clone_from(repo_url, dest_folder)
+        # , but with throwing an exception upon timeout.
+        # Note: This can only be used in context that supports using pipes.
+        subprocess.run([
+            "git", "clone",
+            "--filter=blob:none",
+            "--depth", "1",
+            repo_url, dest_folder
+        ], check=True,  # check=True will raise an exception if the command fails
+            stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL, timeout=operation_timeout_in_seconds)
+
+    CLONE_TIMEOUT_SEC = 20
+    # Clone a given url to a destination folder. If successful, returns an object that wraps the destination folder,
+    # deleting it once it is garbage collected. See: GitProvider.ScopedClonedRepo for more details.
+    def clone(self, repo_url_to_clone: str, dest_folder: str, remove_dest_folder: bool = True,
+              operation_timeout_in_seconds: int=CLONE_TIMEOUT_SEC) -> ScopedClonedRepo|None:
+        returned_obj = None
+        clone_url = self._prepare_clone_url_with_token(repo_url_to_clone)
+        if not clone_url:
+            get_logger().error("Clone failed: Unable to obtain url to clone.")
+            return returned_obj
+        try:
+            if remove_dest_folder and os.path.exists(dest_folder) and os.path.isdir(dest_folder):
+                shutil.rmtree(dest_folder)
+            self._clone_inner(clone_url, dest_folder, operation_timeout_in_seconds)
+            returned_obj = GitProvider.ScopedClonedRepo(dest_folder)
+        except Exception as e:
+            get_logger().exception(f"Clone failed: Could not clone url.",
+                artifact={"error": str(e), "url": clone_url, "dest_folder": dest_folder})
+        finally:
+            return returned_obj
+
     @abstractmethod
     def get_files(self) -> list:
         pass

pr_agent/git_providers/github_provider.py

@@ -5,11 +5,13 @@ import itertools
 import re
 import time
 import traceback
+import json
 from datetime import datetime
 from typing import Optional, Tuple
 from urllib.parse import urlparse
 
-from github import AppAuthentication, Auth, Github
+from github.Issue import Issue
+from github import AppAuthentication, Auth, Github, GithubException
 from retry import retry
 from starlette_context import context
 
@@ -41,6 +43,7 @@ class GithubProvider(GitProvider):
         self.repo = None
         self.pr_num = None
         self.pr = None
+        self.issue_main = None
         self.github_user_id = None
         self.diff_files = None
         self.git_files = None
@@ -50,9 +53,29 @@ class GithubProvider(GitProvider):
             self.pr_commits = list(self.pr.get_commits())
             self.last_commit_id = self.pr_commits[-1]
             self.pr_url = self.get_pr_url() # pr_url for github actions can be as api.github.com, so we need to get the url from the pr object
-        else:
+        elif pr_url and 'issue' in pr_url: #url is an issue
+            self.issue_main = self._get_issue_handle(pr_url)
+        else: #Instantiated the provider without a PR / Issue
             self.pr_commits = None
 
+    def _get_issue_handle(self, issue_url) -> Optional[Issue]:
+        repo_name, issue_number = self._parse_issue_url(issue_url)
+        if not repo_name or not issue_number:
+            get_logger().error(f"Given url: {issue_url} is not a valid issue.")
+            return None
+        # else: Check if can get a valid Repo handle:
+        try:
+            repo_obj = self.github_client.get_repo(repo_name)
+            if not repo_obj:
+                get_logger().error(f"Given url: {issue_url}, belonging to owner/repo: {repo_name} does "
+                                   f"not have a valid repository: {self.get_git_repo_url(issue_url)}")
+                return None
+            # else: Valid repo handle:
+            return repo_obj.get_issue(issue_number)
+        except Exception as e:
+            get_logger().exception(f"Failed to get an issue object for issue: {issue_url}, belonging to owner/repo: {repo_name}")
+            return None
+
     def get_incremental_commits(self, incremental=IncrementalPR(False)):
         self.incremental = incremental
         if self.incremental.is_incremental:
@@ -62,6 +85,63 @@ class GithubProvider(GitProvider):
     def is_supported(self, capability: str) -> bool:
         return True
 
+    def _get_owner_and_repo_path(self, given_url: str) -> str:
+        try:
+            repo_path = None
+            if 'issues' in given_url:
+                repo_path, _ = self._parse_issue_url(given_url)
+            elif 'pull' in given_url:
+                repo_path, _ = self._parse_pr_url(given_url)
+            elif given_url.endswith('.git'):
+                parsed_url = urlparse(given_url)
+                repo_path = (parsed_url.path.split('.git')[0])[1:] # /<owner>/<repo>.git -> <owner>/<repo>
+            if not repo_path:
+                get_logger().error(f"url is neither an issues url nor a pr url nor a valid git url: {given_url}. Returning empty result.")
+                return ""
+            return repo_path
+        except Exception as e:
+            get_logger().exception(f"unable to parse url: {given_url}. Returning empty result.")
+            return ""
+
+    def get_git_repo_url(self, issues_or_pr_url: str) -> str:
+        repo_path = self._get_owner_and_repo_path(issues_or_pr_url) #Return: <OWNER>/<REPO>
+        if not repo_path or repo_path not in issues_or_pr_url:
+            get_logger().error(f"Unable to retrieve owner/path from url: {issues_or_pr_url}")
+            return ""
+        return f"{self.base_url_html}/{repo_path}.git" #https://github.com / <OWNER>/<REPO>.git
+
+    # Given a git repo url, return prefix and suffix of the provider in order to view a given file belonging to that repo.
+    # Example: https://github.com/qodo-ai/pr-agent.git and branch: v0.8 -> prefix: "https://github.com/qodo-ai/pr-agent/blob/v0.8", suffix: ""
+    # In case git url is not provided, provider will use PR context (which includes branch) to determine the prefix and suffix.
+    def get_canonical_url_parts(self, repo_git_url:str, desired_branch:str) -> Tuple[str, str]:
+        owner = None
+        repo = None
+        scheme_and_netloc = None
+
+        if repo_git_url or self.issue_main: #Either user provided an external git url, which may be different than what this provider was initialized with, or an issue:
+            desired_branch = desired_branch if repo_git_url else self.issue_main.repository.default_branch
+            html_url = repo_git_url if repo_git_url else self.issue_main.html_url
+            parsed_git_url = urlparse(html_url)
+            scheme_and_netloc = parsed_git_url.scheme + "://" + parsed_git_url.netloc
+            repo_path = self._get_owner_and_repo_path(html_url)
+            if repo_path.count('/') == 1: #Has to have the form <owner>/<repo>
+                owner, repo = repo_path.split('/')
+            else:
+                get_logger().error(f"Invalid repo_path: {repo_path} from url: {html_url}")
+                return ("", "")
+
+        if (not owner or not repo) and self.repo: #"else" - User did not provide an external git url, or not an issue, use self.repo object
+            owner, repo = self.repo.split('/')
+            scheme_and_netloc = self.base_url_html
+            desired_branch = self.repo_obj.default_branch
+        if not all([scheme_and_netloc, owner, repo]): #"else": Not invoked from a PR context,but no provided git url for context
+            get_logger().error(f"Unable to get canonical url parts since missing context (PR or explicit git url)")
+            return ("", "")
+
+        prefix = f"{scheme_and_netloc}/{owner}/{repo}/blob/{desired_branch}"
+        suffix = ""  # github does not add a suffix
+        return (prefix, suffix)
+
     def get_pr_url(self) -> str:
         return self.pr.html_url
 
@@ -174,6 +254,24 @@ class GithubProvider(GitProvider):
 
             diff_files = []
             invalid_files_names = []
+            is_close_to_rate_limit = False
+
+            # The base.sha will point to the current state of the base branch (including parallel merges), not the original base commit when the PR was created
+            # We can fix this by finding the merge base commit between the PR head and base branches
+            # Note that The pr.head.sha is actually correct as is - it points to the latest commit in your PR branch.
+            # This SHA isn't affected by parallel merges to the base branch since it's specific to your PR's branch.
+            repo = self.repo_obj
+            pr = self.pr
+            try:
+                compare = repo.compare(pr.base.sha, pr.head.sha) # communication with GitHub
+                merge_base_commit = compare.merge_base_commit
+            except Exception as e:
+                get_logger().error(f"Failed to get merge base commit: {e}")
+                merge_base_commit = pr.base
+            if merge_base_commit.sha != pr.base.sha:
+                get_logger().info(
+                    f"Using merge base commit {merge_base_commit.sha} instead of base commit ")
+
             counter_valid = 0
             for file in files:
                 if not is_valid_file(file.filename):
@@ -181,48 +279,36 @@ class GithubProvider(GitProvider):
                     continue
 
                 patch = file.patch
-
-                # allow only a limited number of files to be fully loaded. We can manage the rest with diffs only
-                counter_valid += 1
-                avoid_load = False
-                if counter_valid >= MAX_FILES_ALLOWED_FULL and patch and not self.incremental.is_incremental:
-                    avoid_load = True
-                    if counter_valid == MAX_FILES_ALLOWED_FULL:
-                        get_logger().info(f"Too many files in PR, will avoid loading full content for rest of files")
-
-                if avoid_load:
+                if is_close_to_rate_limit:
                     new_file_content_str = ""
+                    original_file_content_str = ""
                 else:
-                    new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
+                    # allow only a limited number of files to be fully loaded. We can manage the rest with diffs only
+                    counter_valid += 1
+                    avoid_load = False
+                    if counter_valid >= MAX_FILES_ALLOWED_FULL and patch and not self.incremental.is_incremental:
+                        avoid_load = True
+                        if counter_valid == MAX_FILES_ALLOWED_FULL:
+                            get_logger().info(f"Too many files in PR, will avoid loading full content for rest of files")
 
-                if self.incremental.is_incremental and self.unreviewed_files_set:
-                    original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
-                    patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
-                    self.unreviewed_files_set[file.filename] = patch
-                else:
                     if avoid_load:
-                        original_file_content_str = ""
+                        new_file_content_str = ""
                     else:
-                        # The base.sha will point to the current state of the base branch (including parallel merges), not the original base commit when the PR was created
-                        # We can fix this by finding the merge base commit between the PR head and base branches
-                        # Note that The pr.head.sha is actually correct as is - it points to the latest commit in your PR branch.
-                        # This SHA isn't affected by parallel merges to the base branch since it's specific to your PR's branch.
-                        repo = self.repo_obj
-                        pr = self.pr
-                        try:
-                            compare = repo.compare(pr.base.sha, pr.head.sha)
-                            merge_base_commit = compare.merge_base_commit
-                        except Exception as e:
-                            get_logger().error(f"Failed to get merge base commit: {e}")
-                            merge_base_commit = pr.base
-                        if merge_base_commit.sha != pr.base.sha:
-                            get_logger().info(
-                                f"Using merge base commit {merge_base_commit.sha} instead of base commit "
-                                f"{pr.base.sha} for {file.filename}")
-                        original_file_content_str = self._get_pr_file_content(file, merge_base_commit.sha)
+                        new_file_content_str = self._get_pr_file_content(file, self.pr.head.sha)  # communication with GitHub
 
-                    if not patch:
+                    if self.incremental.is_incremental and self.unreviewed_files_set:
+                        original_file_content_str = self._get_pr_file_content(file, self.incremental.last_seen_commit_sha)
                         patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+                        self.unreviewed_files_set[file.filename] = patch
+                    else:
+                        if avoid_load:
+                            original_file_content_str = ""
+                        else:
+                            original_file_content_str = self._get_pr_file_content(file, merge_base_commit.sha)
+                            # original_file_content_str = self._get_pr_file_content(file, self.pr.base.sha)
+                        if not patch:
+                            patch = load_large_diff(file.filename, new_file_content_str, original_file_content_str)
+
 
                 if file.status == 'added':
                     edit_type = EDIT_TYPE.ADDED
@@ -237,9 +323,14 @@ class GithubProvider(GitProvider):
                     edit_type = EDIT_TYPE.UNKNOWN
 
                 # count number of lines added and removed
-                patch_lines = patch.splitlines(keepends=True)
-                num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
-                num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+                if hasattr(file, 'additions') and hasattr(file, 'deletions'):
+                    num_plus_lines = file.additions
+                    num_minus_lines = file.deletions
+                else:
+                    patch_lines = patch.splitlines(keepends=True)
+                    num_plus_lines = len([line for line in patch_lines if line.startswith('+')])
+                    num_minus_lines = len([line for line in patch_lines if line.startswith('-')])
+
                 file_patch_canonical_structure = FilePatchInfo(original_file_content_str, new_file_content_str, patch,
                                                                file.filename, edit_type=edit_type,
                                                                num_plus_lines=num_plus_lines,
@@ -278,10 +369,19 @@ class GithubProvider(GitProvider):
         self.publish_persistent_comment_full(pr_comment, initial_header, update_header, name, final_update_message)
 
     def publish_comment(self, pr_comment: str, is_temporary: bool = False):
+        if not self.pr and not self.issue_main:
+            get_logger().error("Cannot publish a comment if missing PR/Issue context")
+            return None
+
         if is_temporary and not get_settings().config.publish_output_progress:
             get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return None
         pr_comment = self.limit_output_characters(pr_comment, self.max_comment_chars)
+
+        # In case this is an issue, can publish the comment on the issue.
+        if self.issue_main:
+            return self.issue_main.create_comment(pr_comment)
+
         response = self.pr.create_issue_comment(pr_comment)
         if hasattr(response, "user") and hasattr(response.user, "login"):
             self.github_user_id = response.user.login
@@ -464,8 +564,17 @@ class GithubProvider(GitProvider):
             return False
 
     def edit_comment(self, comment, body: str):
-        body = self.limit_output_characters(body, self.max_comment_chars)
-        comment.edit(body=body)
+        try:
+            body = self.limit_output_characters(body, self.max_comment_chars)
+            comment.edit(body=body)
+        except GithubException as e:
+            if hasattr(e, "status") and e.status == 403:
+                # Log as warning for permission-related issues (usually due to polling)
+                get_logger().warning(
+                    "Failed to edit github comment due to permission restrictions",
+                    artifact={"error": e})
+            else:
+                get_logger().exception(f"Failed to edit github comment", artifact={"error": e})
 
     def edit_comment_from_comment_id(self, comment_id: int, body: str):
         try:
@@ -656,11 +765,11 @@ class GithubProvider(GitProvider):
     def _parse_issue_url(self, issue_url: str) -> Tuple[str, int]:
         parsed_url = urlparse(issue_url)
 
-        if 'github.com' not in parsed_url.netloc:
-            raise ValueError("The provided URL is not a valid GitHub URL")
+        if parsed_url.path.startswith('/api/v3'): #Check if came from github app
+            parsed_url = urlparse(issue_url.replace("/api/v3", ""))
 
         path_parts = parsed_url.path.strip('/').split('/')
-        if 'api.github.com' in parsed_url.netloc:
+        if 'api.github.com' in parsed_url.netloc or '/api/v3' in issue_url: #Check if came from github app
             if len(path_parts) < 5 or path_parts[3] != 'issues':
                 raise ValueError("The provided URL does not appear to be a GitHub ISSUE URL")
             repo_name = '/'.join(path_parts[1:3])
@@ -682,9 +791,9 @@ class GithubProvider(GitProvider):
         return repo_name, issue_number
 
     def _get_github_client(self):
-        deployment_type = get_settings().get("GITHUB.DEPLOYMENT_TYPE", "user")
-
-        if deployment_type == 'app':
+        self.deployment_type = get_settings().get("GITHUB.DEPLOYMENT_TYPE", "user")
+        self.auth = None
+        if self.deployment_type == 'app':
             try:
                 private_key = get_settings().github.private_key
                 app_id = get_settings().github.app_id
@@ -694,16 +803,19 @@ class GithubProvider(GitProvider):
                 raise ValueError("GitHub app installation ID is required when using GitHub app deployment")
             auth = AppAuthentication(app_id=app_id, private_key=private_key,
                                      installation_id=self.installation_id)
-            return Github(app_auth=auth, base_url=self.base_url)
-
-        if deployment_type == 'user':
+            self.auth = auth
+        elif self.deployment_type == 'user':
             try:
                 token = get_settings().github.user_token
             except AttributeError as e:
                 raise ValueError(
                     "GitHub token is required when using user deployment. See: "
                     "https://github.com/Codium-ai/pr-agent#method-2-run-from-source") from e
-            return Github(auth=Auth.Token(token), base_url=self.base_url)
+            self.auth = Auth.Token(token)
+        if self.auth:
+            return Github(auth=self.auth, base_url=self.base_url)
+        else:
+            raise ValueError("Could not authenticate to GitHub")
 
     def _get_repo(self):
         if hasattr(self, 'repo_obj') and \
@@ -867,6 +979,84 @@ class GithubProvider(GitProvider):
         except:
             return ""
 
+    def fetch_sub_issues(self, issue_url):
+        """
+        Fetch sub-issues linked to the given GitHub issue URL using GraphQL via PyGitHub.
+        """
+        sub_issues = set()
+
+        # Extract owner, repo, and issue number from URL
+        parts = issue_url.rstrip("/").split("/")
+        owner, repo, issue_number = parts[-4], parts[-3], parts[-1]
+
+        try:
+            # Gets Issue ID from Issue Number
+            query = f"""
+            query {{
+                repository(owner: "{owner}", name: "{repo}") {{
+                    issue(number: {issue_number}) {{
+                        id
+                    }}
+                }}
+            }}
+            """
+            response_tuple = self.github_client._Github__requester.requestJson("POST", "/graphql",
+                                                                               input={"query": query})
+
+            # Extract the JSON response from the tuple and parses it
+            if isinstance(response_tuple, tuple) and len(response_tuple) == 3:
+                response_json = json.loads(response_tuple[2])
+            else:
+                get_logger().error(f"Unexpected response format: {response_tuple}")
+                return sub_issues
+
+
+            issue_id = response_json.get("data", {}).get("repository", {}).get("issue", {}).get("id")
+
+            if not issue_id:
+                get_logger().warning(f"Issue ID not found for {issue_url}")
+                return sub_issues
+
+            # Fetch Sub-Issues
+            sub_issues_query = f"""
+            query {{
+                node(id: "{issue_id}") {{
+                    ... on Issue {{
+                        subIssues(first: 10) {{
+                            nodes {{
+                                url
+                            }}
+                        }}
+                    }}
+                }}
+            }}
+            """
+            sub_issues_response_tuple = self.github_client._Github__requester.requestJson("POST", "/graphql", input={
+                "query": sub_issues_query})
+
+            # Extract the JSON response from the tuple and parses it
+            if isinstance(sub_issues_response_tuple, tuple) and len(sub_issues_response_tuple) == 3:
+                sub_issues_response_json = json.loads(sub_issues_response_tuple[2])
+            else:
+                get_logger().error("Unexpected sub-issues response format", artifact={"response": sub_issues_response_tuple})
+                return sub_issues
+
+            if not sub_issues_response_json.get("data", {}).get("node", {}).get("subIssues"):
+                get_logger().error("Invalid sub-issues response structure")
+                return sub_issues
+    
+            nodes = sub_issues_response_json.get("data", {}).get("node", {}).get("subIssues", {}).get("nodes", [])
+            get_logger().info(f"Github Sub-issues fetched: {len(nodes)}", artifact={"nodes": nodes})
+
+            for sub_issue in nodes:
+                if "url" in sub_issue:
+                    sub_issues.add(sub_issue["url"])
+
+        except Exception as e:
+            get_logger().exception(f"Failed to fetch sub-issues. Error: {e}")
+
+        return sub_issues
+
     def auto_approve(self) -> bool:
         try:
             res = self.pr.create_review(event="APPROVE")
@@ -965,3 +1155,37 @@ class GithubProvider(GitProvider):
                 get_logger().error(f"Failed to process patch for committable comment, error: {e}")
         return code_suggestions_copy
 
+    #Clone related
+    def _prepare_clone_url_with_token(self, repo_url_to_clone: str) -> str | None:
+        scheme = "https://"
+
+        #For example, to clone:
+        #https://github.com/Codium-ai/pr-agent-pro.git
+        #Need to embed inside the github token:
+        #https://<token>@github.com/Codium-ai/pr-agent-pro.git
+
+        github_token = self.auth.token
+        github_base_url = self.base_url_html
+        if not all([github_token, github_base_url]):
+            get_logger().error("Either missing auth token or missing base url")
+            return None
+        if scheme not in github_base_url:
+            get_logger().error(f"Base url: {github_base_url} is missing prefix: {scheme}")
+            return None
+        github_com = github_base_url.split(scheme)[1]  # e.g. 'github.com' or github.<org>.com
+        if not github_com:
+            get_logger().error(f"Base url: {github_base_url} has an empty base url")
+            return None
+        if github_com not in repo_url_to_clone:
+            get_logger().error(f"url to clone: {repo_url_to_clone} does not contain {github_com}")
+            return None
+        repo_full_name = repo_url_to_clone.split(github_com)[-1]
+        if not repo_full_name:
+            get_logger().error(f"url to clone: {repo_url_to_clone} is malformed")
+            return None
+
+        clone_url = scheme
+        if self.deployment_type == 'app':
+            clone_url += "git:"
+        clone_url += f"{github_token}@{github_com}{repo_full_name}"
+        return clone_url

pr_agent/git_providers/gitlab_provider.py

@@ -57,6 +57,47 @@ class GitLabProvider(GitProvider):
             return False
         return True
 
+    def _get_project_path_from_pr_or_issue_url(self, pr_or_issue_url: str) -> str:
+        repo_project_path = None
+        if 'issues' in pr_or_issue_url:
+            #replace 'issues' with 'merge_requests', since gitlab provider does not support issue urls, just to get the git repo url:
+            pr_or_issue_url = pr_or_issue_url.replace('issues', 'merge_requests')
+        if 'merge_requests' in pr_or_issue_url:
+            repo_project_path, _ = self._parse_merge_request_url(pr_or_issue_url)
+        if not repo_project_path:
+            get_logger().error(f"url is not a valid merge requests url: {pr_or_issue_url}")
+            return ""
+        return repo_project_path
+
+    def get_git_repo_url(self, issues_or_pr_url: str) -> str:
+        provider_url = issues_or_pr_url
+        repo_path = self._get_project_path_from_pr_or_issue_url(provider_url)
+        if not repo_path or repo_path not in issues_or_pr_url:
+            get_logger().error(f"Unable to retrieve project path from url: {issues_or_pr_url}")
+            return ""
+        return f"{issues_or_pr_url.split(repo_path)[0]}{repo_path}.git"
+
+    # Given a git repo url, return prefix and suffix of the provider in order to view a given file belonging to that repo.
+    # Example: https://gitlab.com/codiumai/pr-agent.git and branch: t1 -> prefix: "https://gitlab.com/codiumai/pr-agent/-/blob/t1", suffix: "?ref_type=heads"
+    # In case git url is not provided, provider will use PR context (which includes branch) to determine the prefix and suffix.
+    def get_canonical_url_parts(self, repo_git_url:str=None, desired_branch:str=None) -> Tuple[str, str]:
+        repo_path = ""
+        if not repo_git_url and not self.pr_url:
+            get_logger().error("Cannot get canonical URL parts: missing either context PR URL or a repo GIT URL")
+            return ("", "")
+        if not repo_git_url: #Use PR url as context
+            repo_path = self._get_project_path_from_pr_or_issue_url(self.pr_url)
+            try:
+                desired_branch = self.gl.projects.get(self.id_project).default_branch
+            except Exception as e:
+                get_logger().exception(f"Cannot get PR: {self.pr_url} default branch. Tried project ID: {self.id_project}")
+                return ("", "")
+        else: #Use repo git url
+            repo_path = repo_git_url.split('.git')[0].split('.com/')[-1]
+        prefix = f"{self.gitlab_url}/{repo_path}/-/blob/{desired_branch}"
+        suffix = "?ref_type=heads"  # gitlab cloud adds this suffix. gitlab server does not, but it is harmless.
+        return (prefix, suffix)
+
     @property
     def pr(self):
         '''The GitLab terminology is merge request (MR) instead of pull request (PR)'''
@@ -181,7 +222,13 @@ class GitLabProvider(GitProvider):
             get_logger().exception(f"Could not update merge request {self.id_mr} description: {e}")
 
     def get_latest_commit_url(self):
-        return self.mr.commits().next().web_url
+        try:
+            return self.mr.commits().next().web_url
+        except StopIteration: # no commits
+            return ""
+        except Exception as e:
+            get_logger().exception(f"Could not get latest commit URL: {e}")
+            return ""
 
     def get_comment_url(self, comment):
         return f"{self.mr.web_url}#note_{comment.id}"
@@ -472,7 +519,8 @@ class GitLabProvider(GitProvider):
 
     def get_repo_settings(self):
         try:
-            contents = self.gl.projects.get(self.id_project).files.get(file_path='.pr_agent.toml', ref=self.mr.target_branch).decode()
+            main_branch = self.gl.projects.get(self.id_project).default_branch
+            contents = self.gl.projects.get(self.id_project).files.get(file_path='.pr_agent.toml', ref=main_branch).decode()
             return contents
         except Exception:
             return ""
@@ -591,3 +639,24 @@ class GitLabProvider(GitProvider):
                 get_logger().info(f"Failed adding line link, error: {e}")
 
         return ""
+    #Clone related
+    def _prepare_clone_url_with_token(self, repo_url_to_clone: str) -> str | None:
+        if "gitlab." not in repo_url_to_clone:
+            get_logger().error(f"Repo URL: {repo_url_to_clone} is not a valid gitlab URL.")
+            return None
+        (scheme, base_url) = repo_url_to_clone.split("gitlab.")
+        access_token = self.gl.oauth_token
+        if not all([scheme, access_token, base_url]):
+            get_logger().error(f"Either no access token found, or repo URL: {repo_url_to_clone} "
+                               f"is missing prefix: {scheme} and/or base URL: {base_url}.")
+            return None
+
+        #Note that the ""official"" method found here:
+        # https://docs.gitlab.com/user/profile/personal_access_tokens/#clone-repository-using-personal-access-token
+        # requires a username, which may not be applicable.
+        # The following solution is taken from: https://stackoverflow.com/questions/25409700/using-gitlab-token-to-clone-without-authentication/35003812#35003812
+        # For example: For repo url: https://gitlab.codium-inc.com/qodo/autoscraper.git
+        # Then to clone one will issue: 'git clone https://oauth2:<access token>@gitlab.codium-inc.com/qodo/autoscraper.git'
+
+        clone_url = f"{scheme}oauth2:{access_token}@gitlab.{base_url}"
+        return clone_url

pr_agent/git_providers/local_git_provider.py

@@ -141,6 +141,18 @@ class LocalGitProvider(GitProvider):
     def remove_comment(self, comment):
         pass  # Not applicable to the local git provider, but required by the interface
 
+    def add_eyes_reaction(self, comment):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def get_commit_messages(self):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def get_repo_settings(self):
+        pass  # Not applicable to the local git provider, but required by the interface
+
+    def remove_reaction(self, comment):
+        pass  # Not applicable to the local git provider, but required by the interface
+
     def get_languages(self):
         """
         Calculate percentage of languages in repository. Used for hunk prioritisation.

pr_agent/git_providers/utils.py

@@ -12,6 +12,7 @@ from pr_agent.log import get_logger
 
 
 def apply_repo_settings(pr_url):
+    os.environ["AUTO_CAST_FOR_DYNACONF"] = "false"
     git_provider = get_git_provider_with_context(pr_url)
     if get_settings().config.use_repo_settings_file:
         repo_settings_file = None
@@ -101,22 +102,3 @@ def set_claude_model():
     get_settings().set('config.model', model_claude)
     get_settings().set('config.model_weak', model_claude)
     get_settings().set('config.fallback_models', [model_claude])
-
-
-def is_user_name_a_bot(name: str) -> bool:
-    if not name:
-        return False
-    bot_indicators = ['codium', 'bot_', 'bot-', '_bot', '-bot', 'qodo', "service", "github", "jenkins", "auto",
-                      "cicd", "validator", "ci-", "assistant", "srv-"]
-    return any(indicator in name.lower() for indicator in bot_indicators)
-
-
-def is_pr_description_indicating_bot(description: str) -> bool:
-    if not description:
-        return False
-    bot_descriptions = ["Snyk has created this PR", "This PR was created automatically by",
-                        "This PR was created by a bot",
-                        "This pull request was automatically generated by"]
-    # Check is it's a Snyk bot
-    if any(bot_description in description for bot_description in bot_descriptions):
-        return True

pr_agent/log/__init__.py

@@ -1,6 +1,7 @@
+import os
+os.environ["AUTO_CAST_FOR_DYNACONF"] = "false"
 import json
 import logging
-import os
 import sys
 from enum import Enum
 

pr_agent/servers/azuredevops_server_webhook.py

@@ -25,7 +25,7 @@ from pr_agent.config_loader import get_settings
 from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 security = HTTPBasic()
 router = APIRouter()
 available_commands_rgx = re.compile(r"^\/(" + "|".join(command2class.keys()) + r")\s*")
@@ -33,20 +33,16 @@ azure_devops_server = get_settings().get("azure_devops_server")
 WEBHOOK_USERNAME = azure_devops_server.get("webhook_username")
 WEBHOOK_PASSWORD = azure_devops_server.get("webhook_password")
 
-def handle_request(
-    background_tasks: BackgroundTasks, url: str, body: str, log_context: dict
+async def handle_request_comment( url: str, body: str, log_context: dict
 ):
     log_context["action"] = body
     log_context["api_url"] = url
 
-    async def inner():
-        try:
-            with get_logger().contextualize(**log_context):
-                await PRAgent().handle_request(url, body)
-        except Exception as e:
-            get_logger().error(f"Failed to handle webhook: {e}")
-
-    background_tasks.add_task(inner)
+    try:
+        with get_logger().contextualize(**log_context):
+            await PRAgent().handle_request(url, body)
+    except Exception as e:
+        get_logger().exception(f"Failed to handle webhook", artifact={"url": url, "body": body}, error=str(e))
 
 
 # currently only basic auth is supported with azure webhooks
@@ -68,6 +64,9 @@ async def _perform_commands_azure(commands_conf: str, agent: PRAgent, api_url: s
         get_logger().info(f"Auto feedback is disabled, skipping auto commands for PR {api_url=}", **log_context)
         return
     commands = get_settings().get(f"azure_devops_server.{commands_conf}")
+    if not commands:
+        return
+
     get_settings().set("config.is_auto_command", True)
     for command in commands:
         try:
@@ -83,12 +82,7 @@ async def _perform_commands_azure(commands_conf: str, agent: PRAgent, api_url: s
             get_logger().error(f"Failed to perform command {command}: {e}")
 
 
-@router.post("/", dependencies=[Depends(authorize)])
-async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
-    log_context = {"server_type": "azure_devops_server"}
-    data = await request.json()
-    get_logger().info(json.dumps(data))
-
+async def handle_request_azure(data, log_context):
     actions = []
     if data["eventType"] == "git.pullrequest.created":
         # API V1 (latest)
@@ -96,7 +90,10 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
         log_context["event"] = data["eventType"]
         log_context["api_url"] = pr_url
         await _perform_commands_azure("pr_commands", PRAgent(), pr_url, log_context)
-        return
+        return JSONResponse(
+            status_code=status.HTTP_202_ACCEPTED,
+            content=jsonable_encoder({"message": "webhook triggered successfully"})
+        )
     elif data["eventType"] == "ms.vss-code.git-pullrequest-comment-event" and "content" in data["resource"]["comment"]:
         if available_commands_rgx.match(data["resource"]["comment"]["content"]):
             if(data["resourceVersion"] == "2.0"):
@@ -124,7 +121,7 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
 
     for action in actions:
         try:
-            handle_request(background_tasks, pr_url, action, log_context)
+            await handle_request_comment(pr_url, action, log_context)
         except Exception as e:
             get_logger().error("Azure DevOps Trigger failed. Error:" + str(e))
             return JSONResponse(
@@ -135,6 +132,18 @@ async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
         status_code=status.HTTP_202_ACCEPTED, content=jsonable_encoder({"message": "webhook triggered successfully"})
     )
 
+@router.post("/", dependencies=[Depends(authorize)])
+async def handle_webhook(background_tasks: BackgroundTasks, request: Request):
+    log_context = {"server_type": "azure_devops_server"}
+    data = await request.json()
+    # get_logger().info(json.dumps(data))
+
+    background_tasks.add_task(handle_request_azure, data, log_context)
+
+    return JSONResponse(
+        status_code=status.HTTP_202_ACCEPTED, content=jsonable_encoder({"message": "webhook triggered successfully"})
+    )
+
 @router.get("/")
 async def root():
     return {"status": "ok"}

pr_agent/servers/bitbucket_app.py

@@ -19,17 +19,13 @@ from starlette_context.middleware import RawContextMiddleware
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
-from pr_agent.git_providers.utils import apply_repo_settings, is_user_name_a_bot, is_pr_description_indicating_bot
+from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider
 from pr_agent.identity_providers.identity_provider import Eligibility
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
-from pr_agent.servers.github_action_runner import get_setting_or_env, is_true
-from pr_agent.tools.pr_code_suggestions import PRCodeSuggestions
-from pr_agent.tools.pr_description import PRDescription
-from pr_agent.tools.pr_reviewer import PRReviewer
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 router = APIRouter()
 secret_provider = get_secret_provider() if get_settings().get("CONFIG.SECRET_PROVIDER") else None
 
@@ -75,6 +71,18 @@ async def handle_manifest(request: Request, response: Response):
     return JSONResponse(manifest_obj)
 
 
+def _get_username(data):
+    actor = data.get("data", {}).get("actor", {})
+    if actor:
+        if "username" in actor:
+            return actor["username"]
+        elif "display_name" in actor:
+            return actor["display_name"]
+        elif "nickname" in actor:
+            return actor["nickname"]
+    return ""
+
+
 async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_url: str, log_context: dict, data: dict):
     apply_repo_settings(api_url)
     if commands_conf == "pr_commands" and get_settings().config.disable_auto_feedback:  # auto commands for PR, and auto feedback is disabled
@@ -102,22 +110,11 @@ async def _perform_commands_bitbucket(commands_conf: str, agent: PRAgent, api_ur
 def is_bot_user(data) -> bool:
     try:
         actor = data.get("data", {}).get("actor", {})
-        description = data.get("data", {}).get("pullrequest", {}).get("description", "")
         # allow actor type: user . if it's "AppUser" or "team" then it is a bot user
         allowed_actor_types = {"user"}
         if actor and actor["type"].lower() not in allowed_actor_types:
             get_logger().info(f"BitBucket actor type is not 'user', skipping: {actor}")
             return True
-
-        username = actor.get("username", "")
-        if username and is_user_name_a_bot(username):
-            get_logger().info(f"BitBucket actor is a bot user, skipping: {username}")
-            return True
-
-        if description and is_pr_description_indicating_bot(description):
-            get_logger().info(f"Description indicates a bot user: {actor}",
-                              artifact={"description": description})
-            return True
     except Exception as e:
         get_logger().error(f"Failed 'is_bot_user' logic: {e}")
     return False
@@ -129,6 +126,14 @@ def should_process_pr_logic(data) -> bool:
         title = pr_data.get("title", "")
         source_branch = pr_data.get("source", {}).get("branch", {}).get("name", "")
         target_branch = pr_data.get("destination", {}).get("branch", {}).get("name", "")
+        sender = _get_username(data)
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' setting")
+                return False
 
         # logic to ignore PRs with specific titles
         if title:
@@ -178,16 +183,7 @@ async def handle_github_webhooks(background_tasks: BackgroundTasks, request: Req
                     return "OK"
 
             # Get the username of the sender
-            actor = data.get("data", {}).get("actor", {})
-            if actor:
-                try:
-                    username = actor["username"]
-                except KeyError:
-                    try:
-                        username = actor["display_name"]
-                    except KeyError:
-                        username = actor["nickname"]
-                log_context["sender"] = username
+            log_context["sender"] = _get_username(data)
 
             sender_id = data.get("data", {}).get("actor", {}).get("account_id", "")
             log_context["sender_id"] = sender_id

pr_agent/servers/bitbucket_server_webhook.py

@@ -21,7 +21,7 @@ from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import verify_signature
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 router = APIRouter()
 
 

pr_agent/servers/github_action_runner.py

@@ -81,7 +81,7 @@ async def run_action():
         get_logger().info(f"github action: failed to apply repo settings: {e}")
 
     # Handle pull request opened event
-    if GITHUB_EVENT_NAME == "pull_request":
+    if GITHUB_EVENT_NAME == "pull_request" or GITHUB_EVENT_NAME == "pull_request_target":
         action = event_payload.get("action")
 
         # Retrieve the list of actions from the configuration

pr_agent/servers/github_app.py

@@ -18,13 +18,13 @@ from pr_agent.config_loader import get_settings, global_settings
 from pr_agent.git_providers import (get_git_provider,
                                     get_git_provider_with_context)
 from pr_agent.git_providers.git_provider import IncrementalPR
-from pr_agent.git_providers.utils import apply_repo_settings, is_user_name_a_bot, is_pr_description_indicating_bot
+from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.identity_providers import get_identity_provider
 from pr_agent.identity_providers.identity_provider import Eligibility
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.servers.utils import DefaultDictWithTimeout, verify_signature
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 base_path = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
 build_number_path = os.path.join(base_path, "build_number.txt")
 if os.path.exists(build_number_path):
@@ -64,7 +64,7 @@ async def get_body(request):
     try:
         body = await request.json()
     except Exception as e:
-        get_logger().error("Error parsing request body", e)
+        get_logger().error("Error parsing request body", artifact={'error': e})
         raise HTTPException(status_code=400, detail="Error parsing request body") from e
     webhook_secret = getattr(get_settings().github, 'webhook_secret', None)
     if webhook_secret:
@@ -107,7 +107,7 @@ async def handle_comments_on_pr(body: Dict[str, Any],
                 comment_body = handle_line_comments(body, comment_body)
                 disable_eyes = True
         except Exception as e:
-            get_logger().error(f"Failed to handle line comments: {e}")
+            get_logger().error("Failed to get log context", artifact={'error': e})
     else:
         return {}
     log_context["api_url"] = api_url
@@ -138,7 +138,7 @@ async def handle_new_pr_opened(body: Dict[str, Any],
         # logic to ignore PRs with specific titles (e.g. "[Auto] ...")
         apply_repo_settings(api_url)
         if get_identity_provider().verify_eligibility("github", sender_id, api_url) is not Eligibility.NOT_ELIGIBLE:
-                await _perform_auto_commands_github("pr_commands", agent, body, api_url, log_context)
+            await _perform_auto_commands_github("pr_commands", agent, body, api_url, log_context)
         else:
             get_logger().info(f"User {sender=} is not eligible to process PR {api_url=}")
 
@@ -196,8 +196,8 @@ async def handle_push_trigger_for_new_commits(body: Dict[str, Any],
 
     try:
         if get_identity_provider().verify_eligibility("github", sender_id, api_url) is not Eligibility.NOT_ELIGIBLE:
-                get_logger().info(f"Performing incremental review for {api_url=} because of {event=} and {action=}")
-                await _perform_auto_commands_github("push_commands", agent, body, api_url, log_context)
+            get_logger().info(f"Performing incremental review for {api_url=} because of {event=} and {action=}")
+            await _perform_auto_commands_github("push_commands", agent, body, api_url, log_context)
 
     finally:
         # release the waiting task block
@@ -233,27 +233,18 @@ def get_log_context(body, event, action, build_number):
                        "request_id": uuid.uuid4().hex, "build_number": build_number, "app_name": app_name,
                         "repo": repo, "git_org": git_org, "installation_id": installation_id}
     except Exception as e:
-        get_logger().error("Failed to get log context", e)
+        get_logger().error(f"Failed to get log context", artifact={'error': e})
         log_context = {}
     return log_context, sender, sender_id, sender_type
 
 
-def is_bot_user(sender, sender_type, user_description):
+def is_bot_user(sender, sender_type):
     try:
         # logic to ignore PRs opened by bot
-        if get_settings().get("GITHUB_APP.IGNORE_BOT_PR", False):
-            if sender_type.lower() == "bot":
-                if 'pr-agent' not in sender:
-                    get_logger().info(f"Ignoring PR from '{sender=}' because it is a bot")
-                return True
-            if is_user_name_a_bot(sender):
+        if get_settings().get("GITHUB_APP.IGNORE_BOT_PR", False) and sender_type == "Bot":
+            if 'pr-agent' not in sender:
                 get_logger().info(f"Ignoring PR from '{sender=}' because it is a bot")
-                return True
-            # Ignore PRs opened by bot users based on their description
-            if isinstance(user_description, str) and is_pr_description_indicating_bot(user_description):
-                get_logger().info(f"Description indicates a bot user: {sender}",
-                                  artifact={"description": user_description})
-                return True
+            return True
     except Exception as e:
         get_logger().error(f"Failed 'is_bot_user' logic: {e}")
     return False
@@ -266,6 +257,14 @@ def should_process_pr_logic(body) -> bool:
         pr_labels = pull_request.get("labels", [])
         source_branch = pull_request.get("head", {}).get("ref", "")
         target_branch = pull_request.get("base", {}).get("ref", "")
+        sender = body.get("sender", {}).get("login")
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' setting")
+                return False
 
         # logic to ignore PRs with specific titles
         if title:
@@ -285,6 +284,7 @@ def should_process_pr_logic(body) -> bool:
                 get_logger().info(f"Ignoring PR with labels '{labels_str}' due to config.ignore_pr_labels settings")
                 return False
 
+        # logic to ignore PRs with specific source or target branches
         ignore_pr_source_branches = get_settings().get("CONFIG.IGNORE_PR_SOURCE_BRANCHES", [])
         ignore_pr_target_branches = get_settings().get("CONFIG.IGNORE_PR_TARGET_BRANCHES", [])
         if pull_request and (ignore_pr_source_branches or ignore_pr_target_branches):
@@ -310,17 +310,20 @@ async def handle_request(body: Dict[str, Any], event: str):
         event: The GitHub event type (e.g. "pull_request", "issue_comment", etc.).
     """
     action = body.get("action")  # "created", "opened", "reopened", "ready_for_review", "review_requested", "synchronize"
+    get_logger().debug(f"Handling request with event: {event}, action: {action}")
     if not action:
+        get_logger().debug(f"No action found in request body, exiting handle_request")
         return {}
     agent = PRAgent()
     log_context, sender, sender_id, sender_type = get_log_context(body, event, action, build_number)
 
     # logic to ignore PRs opened by bot, PRs with specific titles, labels, source branches, or target branches
-    pr_description = body.get("pull_request", {}).get("body", "")
-    if is_bot_user(sender, sender_type, pr_description) and 'check_run' not in body:
+    if is_bot_user(sender, sender_type) and 'check_run' not in body:
+        get_logger().debug(f"Request ignored: bot user detected")
         return {}
     if action != 'created' and 'check_run' not in body:
         if not should_process_pr_logic(body):
+            get_logger().debug(f"Request ignored: PR logic filtering")
             return {}
 
     if 'check_run' in body:  # handle failed checks

pr_agent/servers/github_polling.py

@@ -13,7 +13,7 @@ from pr_agent.config_loader import get_settings
 from pr_agent.git_providers import get_git_provider
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 NOTIFICATION_URL = "https://api.github.com/notifications"
 
 
@@ -130,12 +130,14 @@ async def is_valid_notification(notification, headers, handled_ids, session, use
                                                       artifact={"comment": comment_body})
                                     return True, handled_ids, comment, comment_body, pr_url, user_tag
 
-                            get_logger().error(f"Failed to fetch comments for PR: {pr_url}")
+                            get_logger().warning(f"Failed to fetch comments for PR: {pr_url}",
+                                                    artifact={"comments": comments})
                             return False, handled_ids
 
         return False, handled_ids
     except Exception as e:
-        get_logger().error(f"Error processing notification: {e}", artifact={"traceback": traceback.format_exc()})
+        get_logger().exception(f"Error processing polling notification",
+                               artifact={"notification": notification, "error": e})
         return False, handled_ids
 
 

pr_agent/servers/gitlab_webhook.py

@@ -15,39 +15,16 @@ from starlette_context.middleware import RawContextMiddleware
 from pr_agent.agent.pr_agent import PRAgent
 from pr_agent.algo.utils import update_settings_from_args
 from pr_agent.config_loader import get_settings, global_settings
-from pr_agent.git_providers.utils import apply_repo_settings, is_user_name_a_bot, is_pr_description_indicating_bot
+from pr_agent.git_providers.utils import apply_repo_settings
 from pr_agent.log import LoggingFormat, get_logger, setup_logger
 from pr_agent.secret_providers import get_secret_provider
 
-setup_logger(fmt=LoggingFormat.JSON, level="DEBUG")
+setup_logger(fmt=LoggingFormat.JSON, level=get_settings().get("CONFIG.LOG_LEVEL", "DEBUG"))
 router = APIRouter()
 
 secret_provider = get_secret_provider() if get_settings().get("CONFIG.SECRET_PROVIDER") else None
 
 
-async def get_mr_url_from_commit_sha(commit_sha, gitlab_token, project_id):
-    try:
-        import requests
-        headers = {
-            'Private-Token': f'{gitlab_token}'
-        }
-        # API endpoint to find MRs containing the commit
-        gitlab_url = get_settings().get("GITLAB.URL", 'https://gitlab.com')
-        response = requests.get(
-            f'{gitlab_url}/api/v4/projects/{project_id}/repository/commits/{commit_sha}/merge_requests',
-            headers=headers
-        )
-        merge_requests = response.json()
-        if merge_requests and response.status_code == 200:
-            pr_url = merge_requests[0]['web_url']
-            return pr_url
-        else:
-            get_logger().info(f"No merge requests found for commit: {commit_sha}")
-            return None
-    except Exception as e:
-        get_logger().error(f"Failed to get MR url from commit sha: {e}")
-        return None
-
 async def handle_request(api_url: str, body: str, log_context: dict, sender_id: str):
     log_context["action"] = body
     log_context["event"] = "pull_request" if body == "/review" else "comment"
@@ -86,24 +63,53 @@ def is_bot_user(data) -> bool:
     try:
         # logic to ignore bot users (unlike Github, no direct flag for bot users in gitlab)
         sender_name = data.get("user", {}).get("name", "unknown").lower()
-        if is_user_name_a_bot(sender_name):
+        bot_indicators = ['codium', 'bot_', 'bot-', '_bot', '-bot']
+        if any(indicator in sender_name for indicator in bot_indicators):
             get_logger().info(f"Skipping GitLab bot user: {sender_name}")
             return True
-        pr_description = data.get('object_attributes', {}).get('description', '')
-        if pr_description and is_pr_description_indicating_bot(pr_description):
-            get_logger().info(f"Description indicates a bot user: {sender_name}",
-                              artifact={"description": pr_description})
-            return True
     except Exception as e:
         get_logger().error(f"Failed 'is_bot_user' logic: {e}")
     return False
 
+def is_draft(data) -> bool:
+    try:
+        if 'draft' in data.get('object_attributes', {}):
+            return data['object_attributes']['draft']
+
+        # for gitlab server version before 16
+        elif 'Draft:' in data.get('object_attributes', {}).get('title'):
+            return True
+    except Exception as e:
+        get_logger().error(f"Failed 'is_draft' logic: {e}")
+    return False
+
+def is_draft_ready(data) -> bool:
+    try:
+        if 'draft' in data.get('changes', {}):
+            if data['changes']['draft']['previous'] == 'true' and data['changes']['draft']['current'] == 'false':
+                return True
+            
+        # for gitlab server version before 16
+        elif 'title' in data.get('changes', {}):
+            if 'Draft:' in data['changes']['title']['previous'] and 'Draft:' not in data['changes']['title']['current']:
+                return True
+    except Exception as e:
+        get_logger().error(f"Failed 'is_draft_ready' logic: {e}")
+    return False
 
 def should_process_pr_logic(data) -> bool:
     try:
         if not data.get('object_attributes', {}):
             return False
         title = data['object_attributes'].get('title')
+        sender = data.get("user", {}).get("username", "")
+
+        # logic to ignore PRs from specific users
+        ignore_pr_users = get_settings().get("CONFIG.IGNORE_PR_AUTHORS", [])
+        if ignore_pr_users and sender:
+            if sender in ignore_pr_users:
+                get_logger().info(f"Ignoring PR from user '{sender}' due to 'config.ignore_pr_authors' settings")
+                return False
 
         # logic to ignore MRs for titles, labels and source, target branches.
         ignore_mr_title = get_settings().get("CONFIG.IGNORE_PR_TITLE", [])
@@ -186,22 +192,48 @@ async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
         # ignore bot users
         if is_bot_user(data):
             return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
-        if data.get('event_type') != 'note': # not a comment
+
+        log_context["sender"] = sender
+        if data.get('object_kind') == 'merge_request':
             # ignore MRs based on title, labels, source and target branches
             if not should_process_pr_logic(data):
                 return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
+            object_attributes = data.get('object_attributes', {})
+            if object_attributes.get('action') in ['open', 'reopen']:
+                url = object_attributes.get('url')
+                get_logger().info(f"New merge request: {url}")
+                if is_draft(data):
+                    get_logger().info(f"Skipping draft MR: {url}")
+                    return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
 
-        log_context["sender"] = sender
-        if data.get('object_kind') == 'merge_request' and data['object_attributes'].get('action') in ['open', 'reopen']:
-            title = data['object_attributes'].get('title')
-            url = data['object_attributes'].get('url')
-            draft = data['object_attributes'].get('draft')
-            get_logger().info(f"New merge request: {url}")
-            if draft:
-                get_logger().info(f"Skipping draft MR: {url}")
-                return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
+                await _perform_commands_gitlab("pr_commands", PRAgent(), url, log_context, data)
+
+            # for push event triggered merge requests
+            elif object_attributes.get('action') == 'update' and object_attributes.get('oldrev'):
+                url = object_attributes.get('url')
+                get_logger().info(f"New merge request: {url}")
+                if is_draft(data):
+                    get_logger().info(f"Skipping draft MR: {url}")
+                    return JSONResponse(status_code=status.HTTP_200_OK, content=jsonable_encoder({"message": "success"}))
+
+                commands_on_push = get_settings().get(f"gitlab.push_commands", {})
+                handle_push_trigger = get_settings().get(f"gitlab.handle_push_trigger", False)
+                if not commands_on_push or not handle_push_trigger:
+                    get_logger().info("Push event, but no push commands found or push trigger is disabled")
+                    return JSONResponse(status_code=status.HTTP_200_OK,
+                                        content=jsonable_encoder({"message": "success"}))
+
+                get_logger().debug(f'A push event has been received: {url}')
+                await _perform_commands_gitlab("push_commands", PRAgent(), url, log_context, data)
+                
+            # for draft to ready triggered merge requests
+            elif object_attributes.get('action') == 'update' and is_draft_ready(data):
+                url = object_attributes.get('url')
+                get_logger().info(f"Draft MR is ready: {url}")
+
+                # same as open MR
+                await _perform_commands_gitlab("pr_commands", PRAgent(), url, log_context, data)
 
-            await _perform_commands_gitlab("pr_commands", PRAgent(), url, log_context, data)
         elif data.get('object_kind') == 'note' and data.get('event_type') == 'note': # comment on MR
             if 'merge_request' in data:
                 mr = data['merge_request']
@@ -213,29 +245,6 @@ async def gitlab_webhook(background_tasks: BackgroundTasks, request: Request):
                     body = handle_ask_line(body, data)
 
                 await handle_request(url, body, log_context, sender_id)
-        elif data.get('object_kind') == 'push' and data.get('event_name') == 'push':
-            try:
-                project_id = data['project_id']
-                commit_sha = data['checkout_sha']
-                url = await get_mr_url_from_commit_sha(commit_sha, gitlab_token, project_id)
-                if not url:
-                    get_logger().info(f"No MR found for commit: {commit_sha}")
-                    return JSONResponse(status_code=status.HTTP_200_OK,
-                                        content=jsonable_encoder({"message": "success"}))
-
-                # we need first to apply_repo_settings
-                apply_repo_settings(url)
-                commands_on_push = get_settings().get(f"gitlab.push_commands", {})
-                handle_push_trigger = get_settings().get(f"gitlab.handle_push_trigger", False)
-                if not commands_on_push or not handle_push_trigger:
-                    get_logger().info("Push event, but no push commands found or push trigger is disabled")
-                    return JSONResponse(status_code=status.HTTP_200_OK,
-                                        content=jsonable_encoder({"message": "success"}))
-
-                get_logger().debug(f'A push event has been received: {url}')
-                await _perform_commands_gitlab("push_commands", PRAgent(), url, log_context, data)
-            except Exception as e:
-                get_logger().error(f"Failed to handle push event: {e}")
 
     background_tasks.add_task(inner, request_json)
     end_time = datetime.now()

pr_agent/servers/help.py

@@ -6,6 +6,7 @@ class HelpMessage:
                 "> - **/improve [--extended]**: Suggest code improvements. Extended mode provides a higher quality feedback.   \n" \
                 "> - **/ask \\<QUESTION\\>**: Ask a question about the PR.   \n" \
                 "> - **/update_changelog**: Update the changelog based on the PR's contents.   \n" \
+                "> - **/help_docs \\<QUESTION\\>**: Given a path to documentation (either for this repository or for a given one), ask a question.   \n" \
                 "> - **/add_docs** 💎: Generate docstring for new components introduced in the PR.   \n" \
                 "> - **/generate_labels** 💎: Generate labels for the PR based on the PR's contents.   \n" \
                 "> - **/analyze** 💎: Automatically analyzes the PR, and presents changes walkthrough for each component.   \n\n" \
@@ -201,3 +202,17 @@ some_config2=...
         output += f"\n\nSee the improve [usage page](https://pr-agent-docs.codium.ai/tools/improve/) for a comprehensive guide on using this tool.\n\n"
 
         return output
+
+
+    @staticmethod
+    def get_help_docs_usage_guide():
+        output = "**Overview:**\n"
+        output += """\
+The help docs tool, named `help_docs`, answers a question based on a given relative path of documentation, either from the repository of this merge request or from a given one."
+It can be invoked manually by commenting on any PR:
+```
+/help_docs "..."
+```
+"""
+        output += f"\n\nSee the [help_docs usage](https://pr-agent-docs.codium.ai/tools/help_docs/) page for a comprehensive guide on using this tool.\n\n"
+        return output