[Bug] Memory files loaded twice in git worktrees causing premature compaction and quota exhaustion

[Bug] Memory files loaded twice in git worktrees causing premature compaction and quota exhaustion

Description

When working inside a git worktree, memory files (.claude/rules/*.md and CLAUDE.md) are loaded twice in the context:

• Once with absolute path (~/path/to/repo/.claude/rules/file.md)
• Once with relative path (.claude/rules/file.md)

This doubles the memory file token usage and causes:

• Context filling up immediately after /clear
• Premature context compaction (every 3-4 messages instead of normal behavior)
• Rapid session and weekly quota exhaustion due to excessive token consumption

Environment

• Claude Code version: 2.1.37
• OS: Linux 6.14.0-123037-tuxedo
• Model: claude-sonnet-4-5-20250929
• Context: Git worktree (~/PhpstormProjects/neo/.worktrees/plan-05-mcp-meilisearch)

Steps to Reproduce

1. Create a git worktree:

``bash
git worktree add .worktrees/my-branch my-branch
``

1. Navigate to the worktree:

``bash
cd .worktrees/my-branch
``

1. Start Claude Code:

``bash
claude
``

1. Run /clear to reset context

1. Immediately run /context to check token usage

Actual Behavior

After /clear, context is already at 73% capacity (146k/200k tokens) with:

• Memory files: 109k tokens (54.5%)
• Messages: 106 tokens (0.1%)
• All .claude/rules/*.md files are listed twice in /context output

Example /context output:

Memory files · /memory
└ ~/PhpstormProjects/neo/CLAUDE.md: 1.1k tokens
└ ~/PhpstormProjects/neo/.claude/rules/00-regles-critiques.md: 1k tokens
└ ~/PhpstormProjects/neo/.claude/rules/01-environnement-docker.md: 351 tokens
[... 32 more files ...]

└ CLAUDE.md: 1.1k tokens                                      ← DUPLICATE
└ .claude/rules/00-regles-critiques.md: 1k tokens             ← DUPLICATE
└ .claude/rules/01-environnement-docker.md: 351 tokens        ← DUPLICATE
[... 32 more duplicates ...]

File verification shows:

• Different inodes (physical files, not symlinks)
• Different MD5 hashes (contents have diverged slightly)
• Same number of files in both locations (35 rules files)

Expected Behavior

Memory files should be loaded once only, either from:

• The worktree location (relative path), OR
• The main repository location (absolute path)

Context after /clear should be ~25-30% capacity (50-60k tokens), not 73%.

Impact

Session Quota Exhaustion

With context at 73% capacity from the start:

• Only ~50k tokens remaining for conversation
• Compaction triggers after 3-4 normal messages
• Compacted context loses recent conversation details
• Session quota exhausted much faster than normal

Weekly Quota Exhaustion

Due to premature compaction and double token loading:

• Each session consumes 2x expected tokens
• Weekly quota depleted in ~50% normal time
• Significant cost impact for users with many worktrees

Investigation Details

File Analysis

# Different inodes (not symlinks)
$ ls -i ~/PhpstormProjects/neo/.worktrees/plan-05-mcp-meilisearch/.claude/rules/00-regles-critiques.md
54944005 ...

$ ls -i ~/PhpstormProjects/neo/.claude/rules/00-regles-critiques.md
50728835 ...

# Different content (MD5)
$ md5sum ~/PhpstormProjects/neo/.worktrees/plan-05-mcp-meilisearch/.claude/rules/*.md | head -3
8c56ba221170c9472ca20be251e88fd8  .../00-regles-critiques.md
b72f1b931986c51aaa79fabc04685dd3  .../01-environnement-docker.md
373ada24edb2cbd8edee9768c670e315  .../02-workflow-git.md

$ md5sum ~/PhpstormProjects/neo/.claude/rules/*.md | head -3
8c56ba221170c9472ca20be251e88fd8  .../00-regles-critiques.md  # Same
b72f1b931986c51aaa79fabc04685dd3  .../01-environnement-docker.md  # Same
373ada24edb2cbd8edee9768c670e315  .../02-workflow-git.md  # Same

Worktree Setup

$ git worktree list
/home/atournayre/PhpstormProjects/neo  [release/v27.0.0]
/home/atournayre/PhpstormProjects/neo/.worktrees/plan-05-mcp-meilisearch  [feature/plan-05-mcp-meilisearch]
# ... 8 other worktrees with same issue

Suggested Fix

The memory file discovery logic should:

1. Detect when running inside a git worktree
2. Load memory files from either worktree or main repo (not both)
3. Deduplicate by file content hash or inode to prevent double-loading

Alternative: Add configuration option to specify which location to use for memory files in worktrees.

Workaround

Temporarily, users can:

1. Delete .claude/ directory from worktree to force loading from main repo only
2. Work from main repository instead of worktrees (not ideal for parallel development)

Additional Context

This issue affects all git worktrees in the project (9 worktrees confirmed with same behavior).

The bug was noticed after recent updates to Claude Code (v2.1.37), suggesting it may be a regression in memory file resolution logic.