Bug: CLAUDE.md files created inside .git directory causing git pull failures

[moyuu-az]

📝 Manual Bug Report

Bug Description

CLAUDE.md files are being created inside the .git/ directory structure, which causes git pull to fail with the error:

fatal: bad object refs/CLAUDE.md
error: github.com:xxx/xxx.git did not send all necessary objects

The following files were found inside .git/:

• .git/refs/CLAUDE.md
• .git/refs/tags/CLAUDE.md
• .git/refs/remotes/origin/CLAUDE.md
• .git/logs/CLAUDE.md
• .git/CLAUDE.md

Git interprets these as invalid references, breaking git operations.

Steps to Reproduce

1. Use Claude Code with claude-mem plugin in a git repository
2. Work normally with various tool calls (Read, Edit, Bash, etc.)
3. Attempt git pull
4. Observe the error: fatal: bad object refs/CLAUDE.md

Expected Behavior

The .git/ directory should be completely excluded from CLAUDE.md auto-generation. According to the documentation, "The project root (folders containing a .git directory) is excluded from auto-generation" - but the .git/ directory itself should also be excluded.

Environment

• Claude-mem version: 9.0.1
• Claude Code version: 2.1.9
• OS: macOS 26.1 (Tahoe)
• Platform: Apple Silicon (arm64)

Workaround

Manually removing the files resolves the issue:

find .git -name "CLAUDE.md" -delete

Setting CLAUDE_MEM_FOLDER_CLAUDEMD_ENABLED to "false" in ~/.claude-mem/settings.json may prevent future occurrences.

Additional Context

• The .gitignore already contains CLAUDE.md, but that doesn't prevent files from being created inside .git/
• This appears to be a path filtering issue where .git/ subdirectories are not being excluded
• Multiple CLAUDE.md files (158+) were also created throughout the project in various subdirectories

[github-actions]

A bug has been identified where CLAUDE.md files are being incorrectly generated within the .git/ directory structure when using the Claude Code and claude-mem plugin, leading to git pull failures with errors related to invalid Git object references. This happens despite the .gitignore file including CLAUDE.md, and the documentation stating that directories containing a .git folder should be excluded from auto-generation. The issue stems from CLAUDE.md files being created in subdirectories of .git/, such as .git/refs/ and .git/logs/, causing Git operations to break. A temporary workaround involves manually deleting these files or disabling the auto-generation of CLAUDE.md files in the settings. This bug highlights a need to improve path filtering to properly exclude .git/ and its subdirectories during CLAUDE.md file generation.

[austinoch]

This is also the case for me as well. CLAUDE_MEM_FOLDER_CLAUDEMD_ENABLED: false is not being respected, and CLAUDE.md files are being created in every directory the plugin touches.

[Glucksberg]

🔧 This issue may be resolved by PR #834

The fix replaces isProjectRoot() with isInsideGitRepo() that walks up parent directories. This prevents CLAUDE.md files from being created in any subdirectory of a git repository.

Main tracking issue: #793

[thedotmack]

Duplicate of #793 and #952. CLAUDE.md files in .git/ are caused by the isProjectRoot() detection bug. Tracking the fix in #793.