Output the same output structure as in npx

```pipx run -e --spec . gen-api-key```

- Add shell script as an alternative to Python for API key generation

docs/docs/core-abilities/fetching_ticket_context.md

@@ -9,9 +9,8 @@ This integration enriches the review process by automatically surfacing relevant
 
 **Ticket systems supported**:
 
-- [GitHub](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#github-issues-integration)
-- [Jira (💎)](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#jira-integration)
-- [Linear (💎)](https://qodo-merge-docs.qodo.ai/core-abilities/fetching_ticket_context/#linear-integration)
+- GitHub
+- Jira (💎)
 
 **Ticket data fetched:**
 
@@ -76,17 +75,13 @@ The recommended way to authenticate with Jira Cloud is to install the Qodo Merge
 
 Installation steps:
 
-1. Go to the [Qodo Merge integrations page](https://app.qodo.ai/qodo-merge/integrations)
-
-2. Click on the Connect **Jira Cloud** button to connect the Jira Cloud app
-
-3. Click the `accept` button.<br>
+1. Click [here](https://auth.atlassian.com/authorize?audience=api.atlassian.com&client_id=8krKmA4gMD8mM8z24aRCgPCSepZNP1xf&scope=read%3Ajira-work%20offline_access&redirect_uri=https%3A%2F%2Fregister.jira.pr-agent.codium.ai&state=qodomerge&response_type=code&prompt=consent) to install the Qodo Merge app in your Jira Cloud instance, click the `accept` button.<br>
 ![Jira Cloud App Installation](https://www.qodo.ai/images/pr_agent/jira_app_installation1.png){width=384}
 
-4. After installing the app, you will be redirected to the Qodo Merge registration page. and you will see a success message.<br>
+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}
 
-5. Now Qodo Merge will be able to fetch Jira ticket context for your PRs.
+3. Now Qodo Merge will be able to fetch Jira ticket context for your PRs.
 
 **2) Email/Token Authentication**
 
@@ -305,45 +300,3 @@ Name your branch with the ticket ID as a prefix (e.g., `ISSUE-123-feature-descri
     [jira]
     jira_base_url = "https://<JIRA_ORG>.atlassian.net"
     ```
-
-## Linear Integration 💎
-
-### Linear App Authentication
-
-The recommended way to authenticate with Linear is to connect the Linear app through the Qodo Merge portal.
-
-Installation steps:
-
-1. Go to the [Qodo Merge integrations page](https://app.qodo.ai/qodo-merge/integrations)
-
-2. Navigate to the **Integrations** tab
-
-3. Click on the **Linear** button to connect the Linear app
-
-4. Follow the authentication flow to authorize Qodo Merge to access your Linear workspace
-
-5. Once connected, Qodo Merge will be able to fetch Linear ticket context for your PRs
-
-### How to link a PR to a Linear ticket
-
-Qodo Merge will automatically detect Linear tickets using either of these methods:
-
-**Method 1: Description Reference:**
-
-Include a ticket reference in your PR description using either:
-- The complete Linear ticket URL: `https://linear.app/[ORG_ID]/issue/[TICKET_ID]`
-- The shortened ticket ID: `[TICKET_ID]` (e.g., `ABC-123`) - requires linear_base_url configuration (see below).
-
-**Method 2: Branch Name Detection:**
-
-Name your branch with the ticket ID as a prefix (e.g., `ABC-123-feature-description` or `feature/ABC-123/feature-description`).
-
-!!! note "Linear Base URL"
-   For shortened ticket IDs or branch detection (method 2), you must configure the Linear base URL in your configuration file under the [linear] section:
-
-   ```toml
-   [linear]
-   linear_base_url = "https://linear.app/[ORG_ID]"
-   ```
-
-   Replace `[ORG_ID]` with your Linear organization identifier.

docs/docs/recent_updates/index.md

@@ -12,11 +12,10 @@ It also outlines our development roadmap for the upcoming three months. Please n
     - **Scan Repo Discussions Tool**: A new tool that analyzes past code discussions to generate a `best_practices.md` file, distilling key insights and recommendations. ([Learn more](https://qodo-merge-docs.qodo.ai/tools/scan_repo_discussions/))
     - **Enhanced Models**: Qodo Merge now defaults to a combination of top models (Claude Sonnet 3.7 and Gemini 2.5 Pro) and incorporates dedicated code validation logic for improved results. ([Details 1](https://qodo-merge-docs.qodo.ai/usage-guide/qodo_merge_models/), [Details 2](https://qodo-merge-docs.qodo.ai/core-abilities/code_validation/))
     - **Chrome Extension Update**: Qodo Merge Chrome extension now supports single-tenant users. ([Learn more](https://qodo-merge-docs.qodo.ai/chrome-extension/options/#configuration-options/))
-    - **Installation Metrics**: Upon installation, Qodo Merge analyzes past PRs for key metrics (e.g., time to merge, time to first reviewer feedback), enabling pre/post-installation comparison to calculate ROI.
-
 
 === "Future Roadmap"
     - **Smart Update**: Upon PR updates, Qodo Merge will offer tailored code suggestions, addressing both the entire PR and the specific incremental changes since the last feedback.
     - **CLI Endpoint**: A new Qodo Merge endpoint will accept lists of before/after code changes, execute Qodo Merge commands, and return the results.
     - **Simplified Free Tier**: We plan to transition from a two-week free trial to a free tier offering a limited number of suggestions per month per organization.
     - **Best Practices Hierarchy**: Introducing support for structured best practices, such as for folders in monorepos or a unified best practice file for a group of repositories.
+    - **Installation Metrics**: Upon installation, Qodo Merge will analyze past PRs for key metrics (e.g., time to merge, time to first reviewer feedback), enabling pre/post-installation comparison to calculate ROI.

docs/docs/tools/review.md

@@ -144,26 +144,16 @@ extra_instructions = "..."
     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.
 
-### Auto-generated PR labels by the Review Tool
+### Auto-generated PR labels from the Review Tool
 
 !!! tip ""
 
-    The `review` can tool automatically add labels to your Pull Requests:
+    The `review` tool automatically adds two specific labels to your Pull Requests:
 
-    - **`possible security issue`**: This label is applied if the tool detects a potential [security vulnerability](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L103) in the PR's code. This feedback is controlled by the 'enable_review_labels_security' flag (default is true).
-    - **`review effort [x/5]`**: This label estimates the [effort](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L90) required to review the PR on a relative scale of 1 to 5, where 'x' represents the assessed effort. This feedback is controlled by the 'enable_review_labels_effort' flag (default is true).
-    - **`ticket compliance`**: Adds a label indicating code compliance level ("Fully compliant" | "PR Code Verified" | "Partially compliant" | "Not compliant") to any GitHub/Jira/Linea ticket linked in the PR. Controlled by the 'require_ticket_labels' flag (default: false). If 'require_no_ticket_labels' is also enabled, PRs without ticket links will receive a "No ticket found" label.
+    - **`possible security issue`**: This label is applied if the tool detects a potential [security vulnerability](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L103) in the PR's code. This feedback is controlled by the 'enable_review_labels_security' flag.
+    - **`review effort [x/5]`**: This label estimates the [effort](https://github.com/qodo-ai/pr-agent/blob/main/pr_agent/settings/pr_reviewer_prompts.toml#L90) required to review the PR on a relative scale of 1 to 5, where 'x' represents the assessed effort. This feedback is controlled by the 'enable_review_labels_effort' flag.
 
-
-### Blocking PRs from merging based on the generated labels
-
-!!! tip ""
-
-    You can configure a CI/CD Action to prevent merging PRs with specific labels. For example, implement a dedicated [GitHub Action](https://medium.com/sequra-tech/quick-tip-block-pull-request-merge-using-labels-6cc326936221).
-
-    This approach helps ensure PRs with potential security issues or ticket compliance problems will not be merged without further review.
-
-    Since AI may make mistakes or lack complete context, use this feature judiciously. For flexibility, users with appropriate permissions can remove generated labels when necessary. When a label is removed, this action will be automatically documented in the PR discussion, clearly indicating it was a deliberate override by an authorized user to allow the merge.
+    Note: The `possible security issue` label highlights potential security risks. You can configure a GitHub Action to [prevent merging](https://medium.com/sequra-tech/quick-tip-block-pull-request-merge-using-labels-6cc326936221) PRs that have this label.
 
 ### Extra instructions
 

pr_agent/git_providers/azuredevops_provider.py

@@ -350,8 +350,7 @@ class AzureDevopsProvider(GitProvider):
             get_logger().debug(f"Skipping publish_comment for temporary comment: {pr_comment}")
             return None
         comment = Comment(content=pr_comment)
-        # Set status to 'active' to prevent auto-resolve (see CommentThreadStatus docs)
-        thread = CommentThread(comments=[comment], thread_context=thread_context, status='active')
+        thread = CommentThread(comments=[comment], thread_context=thread_context, status="closed")
         thread_response = self.azure_devops_client.create_thread(
             comment_thread=thread,
             project=self.workspace_slug,

pr_agent/scripts/qm_endpoint_auth/gen_api_key.py

@@ -0,0 +1,60 @@
+import requests
+import json
+import webbrowser
+
+BASE_URL="https://api.cli.qodo.ai"
+QM_CMD_ENDPOINT_KEY_NAME="qm_cmd_endpoint"
+
+def get_api_key():
+    try:
+        url = f"{BASE_URL}/v1/auth/cli-auth?key_name={QM_CMD_ENDPOINT_KEY_NAME}"
+        # Make HTTP request
+        response = requests.get(url, stream=True,  # For SSE (Server-Sent Events)
+                                headers={'Accept': 'text/event-stream'})
+
+        # Parse Server-Sent Events format
+        # Look for line:
+        # data: {"auth_url":"https:\/\/auth.qodo.ai\/?extensionId=Codium.codium&extensionQuery=<SOME UUID>&uriScheme=cli"}
+        opened_auth_url = False
+        for line in response.iter_lines(decode_unicode=True):
+            if line and line.startswith('data:'):
+                data_json = line.replace('data: ', '', 1)
+                try:
+                    data = json.loads(data_json)
+                    if not opened_auth_url:
+                        if 'auth_url' not in data:
+                            print(f"Expected an auth_url, but couldn't find one.")
+                            return None
+                        print(f"Got url: {data['auth_url']}.")
+                        # Unescape the URL
+                        auth_url = data['auth_url'].replace('\\/', '/')
+                        webbrowser.open(auth_url)
+                        opened_auth_url = True
+                    else:
+                        api_key = data.get('api_key', None)
+                        print(f"Got api key: {api_key}.")
+                        if not api_key:
+                            print(f"Expected an api_key, but couldn't find one.")
+                        return api_key
+                except json.JSONDecodeError as e:
+                    print(f"Error parsing JSON: {e}")
+                    return None
+
+        print("No data line found in response")
+        return None
+
+    except requests.exceptions.RequestException as e:
+        print(f"Error making HTTP request: {e}")
+        return None
+
+def run():
+    """This is the function serving as this file's entry point, as defined in pyproject.toml"""
+    print("Attempting to generate an API Key...")
+
+    api_key = get_api_key()
+    if api_key:
+        print(f"Please use the following API Key: {api_key} when invoking QM endpoint.")
+        print(f"For example: curl -i --header \"Authorization: ApiKey {api_key}\" -X POST https://<QM ENDPOINT SERVER ADDR>/api/v1/qodo_merge_cmd")
+
+if __name__ == "__main__":
+    run()

pr_agent/scripts/qm_endpoint_auth/gen_api_key.sh

@@ -0,0 +1,4 @@
+curl -s --no-buffer "https://api.cli.qodo.ai/v1/auth/cli-auth" | while read line; do
+  [[ $line == data:*auth_url* ]] && open "$(echo "$line" | sed 's/.*"auth_url":"\([^"]*\)".*/\1/' | sed 's/\\//g')"
+  [[ $line == data:*api_key* ]] && echo "✅ Authentication successful! API key saved.\n📋 Your API key: $(echo "$line" | sed 's/.*"api_key":"\([^"]*\)".*/\1/')" && break
+done

pyproject.toml

@@ -44,6 +44,7 @@ include = [
 
 [project.scripts]
 pr-agent = "pr_agent.cli:run"
+gen-api-key = "pr_agent.scripts.qm_endpoint_auth.gen_api_key:run"
 
 [tool.ruff]
 line-length = 120