[BUG] Auto memory system prompt path uses CWD-based path but /memory creates directory at git-root-based path

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report
• [x] I am using the latest version of Claude Code

What's Wrong?

When starting a Claude Code session from a subdirectory of a git repository, the system prompt injects a CWD-based memory path:

~/.claude/projects/-user-work-monorepo-agents-my-agent/memory/

But when running /memory, the directory is created at the git-root-based path:

~/.claude/projects/-user-work-monorepo/memory/

The system prompt also says: "This directory already exists — write to it directly with the Write tool (do not run mkdir or check for its existence)."

Since the CWD-based path doesn't exist and Claude is told not to check, every Write to the memory path silently fails. No auto memories are ever saved for any project where sessions are started from a subdirectory of a git repo.

Session JSONL files are correctly written to the CWD-based project directory, but memory goes to the git-root-based directory — the two paths are inconsistent.

What Should Happen?

The memory path in the system prompt should match the path where /memory actually creates the directory. Either:

1. The system prompt should use the git-root-based path (matching /memory behavior), or
2. /memory should create the directory at the CWD-based path (matching the system prompt), or
3. Both should agree on whichever scoping strategy is intended

Error Messages/Logs

No error messages — the failure is silent. The Write tool simply fails because the target directory doesn't exist, and Claude is instructed not to check or create it.

Steps to Reproduce

1. Have a monorepo structure:

``
/repo-root/ ← git root
/repo-root/agents/my-agent/ ← subdirectory with its own CLAUDE.md
``

1. Start a Claude Code session from the subdirectory:

``bash
cd /repo-root/agents/my-agent
claude
``

1. Observe the system prompt contains:

``
You have a persistent, file-based memory system at
~/.claude/projects/-user-work-repo-root-agents-my-agent/memory/
This directory already exists — write to it directly...
``

1. Run /memory — the directory is created at:

``
~/.claude/projects/-user-work-repo-root/memory/
``

1. Verify the CWD-based memory directory does NOT exist:

``bash
ls ~/.claude/projects/-user-work-repo-root-agents-my-agent/memory/
# → No such file or directory
``

1. Have a conversation where Claude should save a memory. It silently fails because the path in the system prompt doesn't exist.

Claude Code Version: 2.1.119 (Claude Code)

Model: Opus

Is this a regression? I don't know — auto memory may have never worked for subdirectory sessions.

Platform: Anthropic API

Operating System: macOS

Terminal/Shell: iTerm2

Additional Information

• The CWD-based project directory (-user-work-repo-root-agents-my-agent/) does exist and stores session JSONL files correctly — only the memory/ subdirectory is missing
• Across 30+ projects on this machine, only 4 have any saved memories — all of them are standalone git repos, not subdirectories
• autoMemoryEnabled is not explicitly set (defaults to enabled), and CLAUDE_CODE_DISABLE_AUTO_MEMORY env var is not set
• Related but different: #25140 (subagent memory path), #34437 (worktree sharing), #29505 (docs)