[Bug]: Storage cleanup deletes thread checkouts that hold work git status does not show #30998

Area: Storage cleanup (worktree cleanup)

Version: T3 Code 0.1.6, Linux.

Worktree cleanup deletes thread checkouts that hold work git status does not show. Before removing a checkout (by age, settled age, merge or thread deletion) it keeps it only when git status --porcelain --ignore-submodules=none prints a line, or, with worktreeKeepWhen: "any-local-files", when git ls-files --others --ignored --exclude-standard --directory prints an entry other than node_modules/ (localChangesReason in storageCleanup.ts). Related but separate: #23866 (nested worktrees).

Expected behavior. Cleanup keeps a checkout that holds any of:

1. an ignored file (the default uncommitted-changes deletes it; any-local-files keeps it)
2. a commit on no remote (git rev-list HEAD --not --remotes prints a line)
3. an edit hidden by git update-index --assume-unchanged (git ls-files -v prints h)
4. an edit hidden by git update-index --skip-worktree (git ls-files -v prints S)
5. an initialized submodule (git submodule status prints a line not starting with -); today the submodule path is force-removed
6. a failed git read (a non-zero exit from any check above); today a failed read does not block removal

Actual behavior. Observed on a scratch fixture: with any-local-files, checkouts (2), (3) and (4) are removed; with the default, (1) is removed too. Cases (5) and (6) are read from the source, not run.

Steps to reproduce (scratch fixture, run against a second server with its own --base-dir):

1. Make a repo with one commit, a .gitignore containing *.local, and a submodule (git submodule add <a local repo> sub && git commit -m sub).
2. Start six threads with t3 thread start --worktree main --branch <name> <project> "ok".
3. In the checkouts: write notes.local (1); commit a file (2); git update-index --assume-unchanged README then edit README (3); the same with --skip-worktree (4); git submodule update --init (5); leave the sixth clean.
4. Set storageCleanup.worktreeAfterDays to 1, move the thread dates in the state database back 15 days, restart the server, wait past the 60 s settle grace, then edit a storageCleanup value to trigger a pass.
5. List what remains. The clean checkout is correctly removed. (1) to (5) should remain.

Impact. Silent loss of local work: ignored notes, unpushed commits and hidden edits, with no warning or list of what a pass will remove.

Workaround. Set worktreeKeepWhen: "any-local-files" everywhere a policy applies; that covers (1) only. Consider making it the default, or showing the checkouts a pass would remove before it removes them.