fix(git): use git CLI in git_add to avoid GitPython index corruption bug

[schuyler]

Description

GitPython's index.add() has a known bug that corrupts the git index when paths contain ./ prefixes or when . is included in the file list. The bug causes:

• Files appearing with ./ prefix (e.g., ./index.md)
• The .git directory itself being staged
• Corrupted commits requiring git filter-repo to fix

Motivation and Context

The previous implementation only handled the exact case of ["."] but failed to handle [".", "other.md"] or ["./README.md"]. This fix uses repo.git.add() (CLI wrapper) for all cases, which is consistent with how other git operations are implemented in this file and correctly handles all edge cases.

Testing

I have been using the mcp-server-git MCP to allow Claude to edit a private otterwiki. Prior to making this change locally, I was seeing corruption of the Git repository every few commits. Since applying the change about a week ago, I have been using the wiki with Claude every single day and have not seen a single error of any kind.

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 follows 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

References

• index.add('.') adds even .git directory into the index, and adds files also with ./ prefix gitpython-developers/GitPython#375
• repo.index.add('.') adds .git directory gitpython-developers/GitPython#292