afx cleanup reports success but leaves the worktree registered and on disk when it holds untracked files

[waleedkadous]

Observed (2026-09-22, cluesmith/codev, after PR #1710 merged)

afx cleanup -p 1709 printed:

[info] To delete: git branch -d "builder/air-1709"
[ok] Builder builder-air-1709 cleaned up!

but afterwards:

• git worktree list still shows .builders/air-1709 (912 MB on disk, branch builder/air-1709 still checked out there)
• git branch -d builder/air-1709 refuses: "used by worktree"
• a second afx cleanup -p 1709 says Builder not found for project: 1709 — the roster row is gone, so the CLI can no longer reach the worktree it failed to remove

A manual git worktree remove .builders/air-1709 (non-force) fails with "contains modified or untracked files, use --force". The untracked files are only the spawn scaffolding (.builder-prompt.txt, .builder-role.md, .builder-session-id, .builder-start.sh, .claude/hooks/); tracked state was clean and every commit was on origin.

Expected

Either the worktree is actually removed (cleanup owns the scaffolding it wrote, so removing it, or using --force for a worktree whose branch is fully merged and pushed, is correct), or cleanup reports the failure and keeps the roster row so it can be retried — not "cleaned up!" with the worktree intact and the handle deleted.

Notes

• Other lanes cleaned up normally with the same scaffolding present, so the trigger may be something specific here (the .claude/hooks/ directory? a node_modules from the builder's pnpm install --frozen-lockfile?). Worth checking what git worktree remove actually returned and whether its exit code is inspected.
• Related but distinct: afx cleanup: transient post-merge 'Builder not found' lookup miss + ghost roster rows that never reconcile (misleads overlap checks) #1569 (transient post-merge "Builder not found" + ghost roster rows).

[waleedkadous]

Reproduced 2026-09-22 with afx cleanup -p 1724 after PR #1725 merged: "[ok] Builder builder-air-1724 cleaned up!" but the worktree is still registered and on disk, roster row gone. Same profile as the first case: tracked tree clean, every commit on origin, only spawn scaffolding untracked (.builder-*, .claude/hooks/) plus the builder's node_modules. Two for two on AIR lanes that ran pnpm install in the worktree.