Feedback #27: Handle removed/orphaned worktrees gracefully (registry↔filesystem drift) — a missing worktree dir should not break ingest

Merged to master by flower-orchestrator (daemon 29). Worker commit 1c3bce2 (branch flower/140-orphaned-worktrees). Centralized fix at ScansHarnessSessions::indexedPathsForProject() (feeds flower:watch/ingest/ingest-commits/ingest-docs/reprice-usage): worktrees.missing_at mark-stale column (ran on MAIN MySQL, 132ms) — stamped when a registered path vanishes, cleared when it reappears; NEVER auto-prune, so sessions/commits/briefs keep attribution + it's reversible. Worktree model gained isMissing()/existsOnFilesystem()/reconcileFilesystemPresence() (idempotent). Guard reconciles per worktree then skips + Log::warning on missing ones so the rest keep ingesting. ScanProjects catalog pass flags orphans even without an ingest run. Adversarial review PASS: migration sqlite-portable (nullable + index, ->after() no-op); additive-only, no MAIN edits. Full suite green on MAIN: 973 tests / 971 passed / 2 skipped / 0 failed. The guard is command-code (run fresh each scheduler cycle) → live without a Horizon reload; defensive fix, only triggers when a worktree dir is actually missing.

Done. Branch flower/140-orphaned-worktrees (off master), commit 1c3bce2. Idle — not merging; orchestrator reviews. What changed (registry↔filesystem drift → ingest never breaks on a vanished worktree dir): - DB: new nullable `worktrees.missing_at` (+ index) — migration 2026_07_04_120000. Stamped when the recorded path no longer exists on disk, cleared when it reappears. Mark-stale, NEVER auto-prune, so sessions/commits/briefs keep attribution (chose flag over deregister for the auto-prune-vs-mark-stale policy). - app/Models/Worktree.php: `isMissing()`, `existsOnFilesystem()`, `reconcileFilesystemPresence()` (stamp/clear missing_at, returns existence; idempotent — only writes on flag flip). The drift policy lives on the model per the task. - app/Console/Commands/Concerns/ScansHarnessSessions.php::indexedPathsForProject — the single chokepoint feeding flower:watch, flower:ingest, flower:ingest-commits, flower:ingest-docs, flower:reprice-usage. Now reconciles each worktree and skips + Log::warning("Skipping missing worktree path during ingest scan") on missing ones, so the other worktrees keep ingesting instead of throwing. CommitIngestService's existing is_dir guard (FLOWER-12 / todo 681) stays as defense-in-depth. - app/Console/Commands/ScanProjects.php: catalog pass reconciles all rows per project so orphans get flagged even without an ingest run, and reappeared ones un-flag (brief item b). Coverage: verified every worktree-path-iterating scheduled consumer routes through indexedPathsForProject (Watch/Ingest/IngestCommits/IngestDocs/RepriceUsage); IngestBacklog doesn't touch worktree paths. Tests (tests/Feature/IngestCommitsCommandTest.php): (1) orphaned worktree flagged (missing_at set + isMissing()) + skipped while root and a live worktree still ingest, no throw; (2) reappeared worktree clears missing_at on next scan. Gates: MEILISEARCH_KEY=LARAVEL-HERD ~/bin/php artisan test → 967 passed / 1 pre-existing skip. Pint clean on all changed files. Isolated worktree DB; no daemons started; did not touch MAIN or its DB (orchestrator runs the migration on merge).

Feedback #27 Authority: OPERATOR APPROVAL REQUIRED Funnel: A - operator approved brief Gate: this brief must not be dispatchable until the operator approves it. Kind: idea Source: flower-ops Summary: Handle removed/orphaned worktrees gracefully (registry↔filesystem drift) — a missing worktree dir should not break ingest Detail: Worktrees get removed in many normal scenarios (worktree-manager remove, manual rm, merged+cleaned branches), leaving the worktree DB row orphaned — registry↔filesystem drift. Today an orphaned row breaks flower:ingest-commits: CommitIngestService.php:35 Process::path($path)->run() throws on a missing cwd (no is_dir guard), aborting the WHOLE ingest batch (surfaced as FLOWER-12 / FLOWER-9). The immediate is_dir guard is already routed (todo 681, preventive/low-urgency). THIS item is the LONG-TERM graceful handling, to refine before building: (a) guard ALL worktree-path consumers against missing dirs (ingest-commits, ingest-docs, harness/session scan — anything iterating worktrees->path); (b) reconcile/prune orphaned worktree rows (e.g. in ScanProjects) with an explicit auto-prune-vs-mark-stale policy; (c) decide per-scenario whether a missing worktree should be skipped, deregistered, or flagged. Good first candidate for the feedback→brief funnel (see the feedback-funnels brief). Context JSON: { "scope": "long-term graceful handling; refine before build", "related_sentry": [ "FLOWER-12", "FLOWER-9" ], "immediate_fix_spec": 1025, "immediate_fix_todo": 681 }