Update Docs: Company Codebase Overview, RAG Integration & Configuration

[ofir-frd]

User description

This PR updates:

• The Company Codebase documentation with an overview of its purpose and how it leverages RAG for enhanced pull request insights.
• Adds detailed configuration instructions and outlines limitations to help users set up the feature more effectively.

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PR Type

Documentation

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Description

• Added detailed documentation for the Company Codebase feature.

• Explained RAG integration, configuration, and limitations.

• Updated navigation links to include Company Codebase.

• Fixed a typo in the Qodo Merge models documentation.

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Changes walkthrough 📝

	Relevant files
Documentation	code_oriented_yaml.md Removed placeholder `Code-oriented YAML` documentation      docs/docs/core-abilities/code_oriented_yaml.md Removed the placeholder documentation for Code-oriented YAML. +0/-2      company_codebase.md Added documentation for `Company Codebase` feature              docs/docs/core-abilities/company_codebase.md Added new documentation for the Company Codebase feature. Explained its purpose, RAG integration, and configuration options. Highlighted limitations and requirements for using the feature. +53/-0    index.md Updated navigation link to `Company Codebase`                        docs/docs/core-abilities/index.md Updated the navigation link to replace Code-oriented YAML with Company Codebase. +1/-1      qodo_merge_models.md Fixed typo in Qodo Merge models documentation                        docs/docs/usage-guide/qodo_merge_models.md Fixed a typo in the description of the default model used by Qodo Merge. +1/-1
Configuration changes	mkdocs.yml Updated navigation to include `Company Codebase`                  docs/mkdocs.yml Updated the navigation structure to include Company Codebase documentation. +1/-1

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PR Code Suggestions ✨

Latest suggestions up to d6f79f4

Category	Suggestion	Impact
General	Include all configuration options The TOML configuration example should include both available options (enable_rag and rag_repo_list) to provide a complete reference, since both are mentioned in the options table below. docs/docs/core-abilities/company_codebase.md [24-27] ``` toml [rag_arguments] -enable_rag=true +enable_rag=true +rag_repo_list=['all'] # or ['my-org/my-repo', ...] - [ ] **Apply this suggestion** <!-- /improve --apply_suggestion=0 --> <details><summary>Suggestion importance[1-10]: 7</summary> __ Why: Adding the 'rag_repo_list' option to the configuration example improves documentation completeness and helps users understand how to configure both available options, making it more practical and user-friendly. </details></details></td><td align=center>Medium </td></tr><tr><td rowspan=1>Learned<br>best practice</td> <td> <details><summary>Enhance configuration documentation with security warnings and considerations when enabling features that access sensitive company data</summary> ___ **Add security-related documentation and warnings about the RAG configuration, <br>especially since it involves accessing and indexing company codebase data. <br>Include information about access controls and data privacy considerations.** [docs/docs/core-abilities/company_codebase.md [25-26]](https://github.com/qodo-ai/pr-agent/pull/1648/files#diff-454c3bd83d82ab38f812b4f5884aa9edd1961e9b6c38ea486fc6c19b551d93ebR25-R26) ```diff [rag_arguments] -enable_rag=true +# Security Note: Ensure proper access controls are in place before enabling RAG +# This feature requires secure database implementation and proper authentication +enable_rag=true # Enable only after reviewing security implications Apply this suggestion Suggestion importance[1-10]: 6	Low
More

• Author self-review: I have reviewed the PR code suggestions, and addressed the relevant ones.

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Previous suggestions

Suggestions up to commit d6f79f4

Category	Suggestion	Impact
Learned best practice	Add security warnings to configuration examples that could expose sensitive codebase access The configuration example should include security warnings about storing sensitive configuration values. Since this feature involves codebase access and potentially sensitive code retrieval, add security notes about protecting this configuration file and using environment variables where appropriate. docs/docs/core-abilities/company_codebase.md [24-27] ``` toml +# Security Note: Ensure this configuration file has appropriate access restrictions +# Consider using environment variables for sensitive settings in production [rag_arguments] -enable_rag=true +enable_rag=true <!-- /improve --apply_suggestion=0 --> <details><summary>Suggestion importance[1-10]: 6</summary> </details></details></td><td align=center>Low </td></tr><tr><td rowspan=1>General</td> <td> <details><summary>Fix TOML syntax formatting</summary> ___ **The TOML configuration syntax is incorrect. TOML uses equals sign for assignment <br>but requires proper spacing and typically uses quotes for boolean values.** [docs/docs/core-abilities/company_codebase.md [24-27]](https://github.com/qodo-ai/pr-agent/pull/1648/files#diff-454c3bd83d82ab38f812b4f5884aa9edd1961e9b6c38ea486fc6c19b551d93ebR24-R27) ```diff ``` toml [rag_arguments] -enable_rag=true +enable_rag = true <!-- /improve --apply_suggestion=1 --> <details><summary>Suggestion importance[1-10]: 5</summary> __ Why: The suggestion correctly identifies a formatting issue in the TOML configuration example. While the original would likely work in most TOML parsers, the improved version with proper spacing around the equals sign follows standard TOML formatting conventions, improving readability and consistency. </details></details></td><td align=center>Low </td></tr> <tr><td align="center" colspan="2"> <!-- /improve --more_suggestions=true --> </td><td></td></tr></tbody></table> </details> <details><summary>✅ Suggestions up to commit b0ed584</summary> <br><table><thead><tr><td><strong>Category</strong></td><td align=left><strong>Suggestion&nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; &nbsp; </strong></td><td align=center><strong>Impact</strong></td></tr><tbody><tr><td rowspan=1>Learned<br>best practice</td> <td> <details><summary>Add security warnings to configuration examples that might contain sensitive information<!-- not_implemented --></summary> ___ **The configuration example should include security warnings about not committing <br>sensitive configuration to version control. Since RAG features may involve <br>access to private codebases, it's important to emphasize proper security <br>practices when showing configuration examples.** [docs/docs/core-abilities/company_codebase.md [24-27]](https://github.com/qodo-ai/pr-agent/pull/1648/files#diff-454c3bd83d82ab38f812b4f5884aa9edd1961e9b6c38ea486fc6c19b551d93ebR24-R27) ```diff +# Security Warning: Store sensitive configuration in environment variables or secure credential managers +# Add configuration files with sensitive data to your .gitignore [rag_arguments] -enable_rag=true +enable_rag=true Suggestion importance[1-10]: 6	Low
General	✅ Fix configuration format Suggestion Impact: The commit partially implemented the suggestion by changing the code block type, though it used 'toml' instead of 'ini' as suggested. The spacing around the equals sign was not changed. code diff: -``` +``` toml The configuration example uses an incorrect format. Configuration files typically use either INI format with equals signs or TOML format with proper syntax. The current format mixes these styles. docs/docs/core-abilities/company_codebase.md [24-27] -``` +```ini [rag_arguments] -enable_rag=true +enable_rag = true `[Suggestion has been applied]` <details><summary>Suggestion importance[1-10]: 5</summary> __ Why: The suggestion correctly identifies a minor formatting issue in the configuration example. Adding proper spacing around the equals sign improves readability and follows standard INI file formatting conventions, which is a good practice for documentation. </details></details></td><td align=center>Low </td></tr> <tr><td align="center" colspan="2"> <!-- /improve --more_suggestions=true --> </td><td></td></tr></tbody></table> </details>