fix: correct add logic for all vs specific files and add tests (#2373)

[tajbaba999]

Description

This PR updates the git_add function to correctly differentiate between staging all files (["."]) and specific files. Previously, using ["."] could unintentionally include the .git/ directory, potentially corrupting the repository. This fix ensures only appropriate files are staged.

It also includes two additional test cases:

• One for adding all files using ["."]
• One for adding specific files only

Server Details

• Server: github
• Changes to: tools

Motivation and Context

Fixes #2373

The issue identified that git_add(files=["."]) was tracking files inside the .git/ directory. This caused repository integrity issues. This PR corrects the logic to avoid touching internal Git files and ensures safe staging behavior.

How Has This Been Tested?

• Verified manually that .git/ is excluded when staging all files
• Added and ran unit tests for both general and specific file staging
• Confirmed behavior works correctly with an LLM client environment

Breaking Changes

None

Types of changes

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to change)
• Documentation update

Checklist

• I have read the MCP Protocol Documentation
• My changes follow MCP security best practices
• I have updated the server's README accordingly
• I have tested this with an LLM client
• My code follows the repository's style guidelines
• New and existing tests pass locally
• I have added appropriate error handling
• I have documented all environment variables and configuration options

Additional context

Let me know if there are any changes or improvements you'd like to see. Happy to revise as needed.

[tajbaba999]

Hello @olaservo,
Please let me know if any changes or improvements are needed. I’ll be happy to make the necessary updates.