fix: bound SQLite WAL growth and prevent worker hangs (#49)

The worker's SQLite WAL could grow unbounded (observed 19MB) and wedge the
DB, hanging Claude Code on every prompt. No checkpoint ever truncated the
WAL (only PASSIVE auto-checkpoint, which cannot reclaim the file), the
connection-scoped pragmas were set via a single Exec so only one pooled
connection received them (e.g. busy_timeout=0 on the rest), and the
maintenance service that would optimize/checkpoint was never wired up.

- Register a sqlite3 ConnectHook driver so all pragmas (busy_timeout,
  journal_mode, synchronous, cache_size, foreign_keys, journal_size_limit)
  apply to every pooled connection; enable safe connection recycling.
- Add Store.Checkpoint (TRUNCATE), checkpoint-on-Close, and a periodic
  size-gated checkpoint loop with configurable interval/threshold.
- Wire up the previously-dead maintenance service; make trigger_maintenance
  actually run DB maintenance instead of only recalculating scores.
- Harden the user-prompt hook to honor its deadline and fail open so a
  slow worker can never stall a prompt.
- Add regression tests for WAL truncation, checkpoint-on-close, and
  per-connection pragmas.

internal/worker/handlers_scoring.go

@@ -314,6 +314,49 @@ func (s *Service) handleTriggerRecalculation(w http.ResponseWriter, r *http.Requ
 	writeJSON(w, map[string]string{"status": "recalculation triggered"})
 }
 
+// handleRunMaintenance triggers an immediate, synchronous database maintenance run
+// (Optimize/TRUNCATE checkpoint + prompt cleanup + any enabled retention/stale cleanup)
+// and also kicks off an importance-score recalculation in the background so the behavior
+// of the previous trigger_maintenance tool is preserved (issue #49).
+func (s *Service) handleRunMaintenance(w http.ResponseWriter, r *http.Request) {
+	// initMu.RLock held by requireReady middleware
+	maintSvc := s.maintenanceSvc
+	recalculator := s.recalculator
+
+	if maintSvc == nil {
+		http.Error(w, "maintenance service not available", http.StatusServiceUnavailable)
+		return
+	}
+
+	// Run maintenance synchronously with an independent, bounded context so the caller
+	// receives a real completion status. Use context.Background so an HTTP client timeout
+	// does not abort an in-progress DB maintenance pass.
+	mctx, cancel := context.WithTimeout(context.Background(), 60*time.Second)
+	defer cancel()
+	maintSvc.RunNowSync(mctx)
+
+	// Preserve prior trigger_maintenance behavior: also recalculate importance scores.
+	recalcTriggered := false
+	if recalculator != nil {
+		recalcTriggered = true
+		s.wg.Add(1)
+		go func() {
+			defer s.wg.Done()
+			ctx, cancel := context.WithTimeout(context.Background(), 60*time.Second)
+			defer cancel()
+			if err := recalculator.RecalculateNow(ctx); err != nil {
+				log.Error().Err(err).Msg("Background recalculation during maintenance failed")
+			}
+		}()
+	}
+
+	writeJSON(w, map[string]any{
+		"status":            "maintenance completed",
+		"recalc_triggered":  recalcTriggered,
+		"maintenance_stats": maintSvc.Stats(),
+	})
+}
+
 // parseIntParam parses an integer query parameter with a default value.
 func parseIntParam(r *http.Request, name string, defaultVal int) int {
 	if val := r.URL.Query().Get(name); val != "" {