CLAUDE.md file creation causes Python package shadowing when working in subdirectories

[nyflyer]

When working in a subdirectory of a Python package, Claude Mem creates CLAUDE.md files using relative paths that recreate the parent directory structure. This creates a local folder with the same name as the installed package, causing Python's import system to find the empty local folder instead of the real package.

Steps to Reproduce:

1. Have a Python package installed (e.g., my_package) as editable
2. Navigate to a subdirectory: my_package/subdir/study/
3. Use Claude Code with Claude Mem plugin
4. Claude Mem attempts to write CLAUDE.md to track another folder in the repo
5. A local ./my_package/ folder is created relative to CWD
6. Imports like from my_package import ... fail with ModuleNotFoundError

Expected Behavior:
CLAUDE.md files should be written using absolute paths, or to a location that doesn't recreate parent directory names

Actual Behavior:
Relative paths create shadowing directories that break Python imports.

Workaround:
rm -rf ./my_package # from the subdirectory where shadowing occurred

Impact: High - breaks all package imports until manually removed

Version: 9.0.4

[itinance]

In my case, i always work in the same base directory for my backend. But it created so many CLAUDE.md files in directories that never existed before. Claude-mem replicated the overall structure of directories in my mono-repository:

❯ find . -iname "CLAUDE.md"
./app/contexts/CLAUDE.md
./supabase/migrations/CLAUDE.md
./components/filter-dialog/CLAUDE.md
./components/protocol/CLAUDE.md
./components/CLAUDE.md
./hooks/CLAUDE.md
./apps/backend/app/api/routers/CLAUDE.md
./apps/backend/tests/unit/api/CLAUDE.md
./apps/backend/supabase/migrations/CLAUDE.md
./apps/backend/CLAUDE.md
./CLAUDE.md

I am already in the directory apps/backend. Claude-mem generated a nested apps/backend directory, and created a hooks-directory, components and many more that never existed before in my project.

It is blowing up CLAUDE.md files with the following content:

<claude-mem-context>
# Recent Activity

<!-- This section is auto-generated by claude-mem. Edit content outside the tags. -->

### Jan 13, 2026

| ID | Time | T | Title | Read |
|----|------|---|-------|------|
| #127 | 2:29 AM | 🔵 | Code Review Findings for Protocol and Filter Components | ~598 |
</claude-mem-context>

[nyflyer]

Yes thank you for linking those bug reports. I want to note that I am on version 9.0.4

[nyflyer]

I think I found a workaround. You basically have to make sure that Claude Code doesn't change its working directory into a subdirectory. If Claude Code is always operating from the root directory, then Claude Mem writes the files appropriately without creating the shadow folders. Either way, it's a bug that needs to be fixed on the Claude Mem side.

[alextakitani]

I have the same problem, Claude.md files everywhere

[hidari]

I encountered a related issue where CLAUDE.md was created inside .git/refs/heads/feature/CLAUDE.md. This corrupts the Git repository structure because Git expects files in .git/refs/heads/ to contain 40-character commit hashes (OIDs), not markdown content.
The workaround is to manually delete the file, but writing files inside .git/ is a pretty serious bug since it can break Git tooling.

[hidari]

Hi, I've been experiencing a critical issue related to this bug.

The Problem:
In my case, CLAUDE.md files are being created inside .git/ directories, such as:

• .git/refs/heads/CLAUDE.md

This corrupts the git repository entirely, which has been quite frustrating.

Root Cause:
The isValidPathForClaudeMd() function in src/utils/claude-md-utils.ts doesn't exclude
paths inside .git/ directories. The existing isProjectRoot() check only verifies if a
folder contains .git, not if the path is inside .git/.

Suggested Fix:
Adding these checks to isValidPathForClaudeMd() should prevent this issue:

// Reject paths inside .git/ directory (prevents corrupting git repos)
if (filePath.includes('/.git/') || filePath.includes('\\.git\\') ||
    filePath.startsWith('.git/') || filePath.startsWith('.git\\')) {
  return false;
}

// Also consider excluding node_modules/
if (filePath.includes('/node_modules/') || filePath.includes('\\node_modules\\') ||
    filePath.startsWith('node_modules/') || filePath.startsWith('node_modules\\')) {
  return false;
}

I'd be happy to submit a PR if that would be helpful. Thank you for your work on this
project!

[itinance]

Hi, I've been experiencing a critical issue related to this bug.

The Problem: In my case, CLAUDE.md files are being created inside .git/ directories, such as:

• .git/refs/heads/CLAUDE.md

This corrupts the git repository entirely, which has been quite frustrating.

Root Cause: The isValidPathForClaudeMd() function in src/utils/claude-md-utils.ts doesn't exclude paths inside .git/ directories. The existing isProjectRoot() check only verifies if a folder contains .git, not if the path is inside .git/.

Suggested Fix: Adding these checks to isValidPathForClaudeMd() should prevent this issue:

// Reject paths inside .git/ directory (prevents corrupting git repos)
if (filePath.includes('/.git/') || filePath.includes('\.git\') ||
filePath.startsWith('.git/') || filePath.startsWith('.git\')) {
return false;
}

// Also consider excluding node_modules/
if (filePath.includes('/node_modules/') || filePath.includes('\node_modules\') ||
filePath.startsWith('node_modules/') || filePath.startsWith('node_modules\')) {
return false;
}

I'd be happy to submit a PR if that would be helpful. Thank you for your work on this
project!

nice catch, thanks for this. However, shouldn't the claude.md file placed nowhere else besides the root-folder? It is not only git .git-folder, where claude.md should never be placed by all means. To my current understanding, there should be always only one claude.md (cvurrently, it populates many directories - even empty one, which have been newly created by this plugin, to place an (almost) empty claude.md

[hidari]

Thanks for the input! Just a heads up — nested CLAUDE.md files are actually an officially supported feature. The Anthropic best practices doc mentions it's especially useful for monorepos, where both root/CLAUDE.md and root/foo/CLAUDE.md get loaded automatically.
That said, yeah, the plugin creating empty CLAUDE.md files everywhere does sound like a separate issue worth looking into!

[nyflyer]

@hidari Yes not pushing back against the nested Claude.MD files, just pointing out that they were created in the wrong directories.

Essentially if Claude Code moved directories down within the repo, Claude Mem then creates phantom directories assuming we're still operating in the root.

E.g.

Repo structure

root/directory/sub_directory

if you CC moves into directory

then claude-mem attempts to create claude.MD files in /root/directory/root/directory which is is wrong. It should always use absolute paths not relative paths.

[hidari]

@nyflyer I see what you mean now. Got it. Thanks.