docs: update configuration options and improve wiki documentation clarity

docs/docs/tools/improve.md

@@ -122,10 +122,10 @@ Use triple quotes to write multi-line instructions. Use bullet points or numbers
 
 > `💎 feature. Platforms supported: GitHub, GitLab, Bitbucket`
 
-Another option to give additional guidance to the AI model is by creating a `best_practices.md` file, either in your repository's root directory or as a [**wiki page**](https://github.com/Codium-ai/pr-agent/wiki) (we recommend the wiki page, as editing and maintaining it over time is easier).
+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. 

docs/docs/usage-guide/configuration_options.md

@@ -87,7 +87,8 @@ Create a dedicated project to hold a global configuration file that affects all
 
 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.
+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.
 

docs/docs/usage-guide/enabling_a_wiki.md

@@ -6,7 +6,6 @@ For optimal functionality of Qodo Merge, we recommend enabling a wiki for each r
 **Key Wiki Features: 💎**
 
 - Storing a [configuration file](https://qodo-merge-docs.qodo.ai/usage-guide/configuration_options/#wiki-configuration-file)
-- Defining a [`best_practices.md`](https://qodo-merge-docs.qodo.ai/tools/improve/#best-practices) 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
 
@@ -26,7 +25,7 @@ To enable a wiki for your repository:
 ### 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 and best practices.
+- 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