hygiene: codemap leaves .codemap/ state in every repo it touches, unignored and sometimes committed; agent worktrees pollute scans

[JordanCoin]

Symptoms, measured 2026-09-04 on one machine

• Every repository under that a hook or scan touched has a .codemap/ directory. In at least 10 repos it shows as untracked in git status because nothing ever added it to an ignore list.
• In business-skills, .codemap/agent_edits.jsonl and .codemap/status were committed, and they change on every session, so every later commit carries state churn.
• codemap . on this repo counted watch/testdata five times because agent worktrees under .claude/worktrees/ are scanned; that produced a wrong before/after figure in PR feat(scanner): Skip testdata directories by default #179's original body.
• The reputation this earns: "codemap leaves a lot behind."

Proposed fix

1. State goes somewhere the repo does not see. Prefer a per-repo directory under the user cache ($XDG_CACHE_HOME/codemap/<hash of repo root>/), or, if the in-repo location must stay, write .codemap/ into .git/info/exclude on first use so it is ignored without touching a tracked .gitignore.
2. codemap setup and codemap doctor report any tracked .codemap/* files and offer git rm --cached.
3. Ignore .claude/worktrees/ and .git/ worktree checkouts by default in the walker, alongside vendor and testdata.
4. Hooks must never create .codemap/ in a repo that has no codemap config and was only visited by a scan (e.g. a one-off codemap . in someone else's project).

Exit test

Fresh clone of any repo, run codemap ., run a session with hooks, then git status --porcelain is empty and codemap . file counts match git ls-files | wc -l modulo ignore rules.

Related: #179, #183, #172.

🤖 Generated with Claude Code

https://claude.ai/code/session_01TcyheQmM3HCvxF5wRL3s5t