Remove obsolete renumber and stale commands, fix test

- Remove renumber.go: Hash IDs eliminated need for ID compaction
- Remove stale.go: Executor/heartbeat tables were never implemented
- Fix TestListCommand: duplicate dependency constraint violation
- Update comments removing references to removed commands

Amp-Thread-ID: https://ampcode.com/threads/T-3dcd8681-c7d3-4fe1-9750-b38279b56cdb
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/main.go

@@ -60,7 +60,7 @@ var (
 	// Auto-flush state
 	autoFlushEnabled  = true  // Can be disabled with --no-auto-flush
 	isDirty           = false // Tracks if DB has changes needing export
-	needsFullExport   = false // Set to true when IDs change (renumber, rename-prefix)
+	needsFullExport   = false // Set to true when IDs change (e.g., rename-prefix)
 	flushMutex        sync.Mutex
 	flushTimer        *time.Timer
 	storeMutex        sync.Mutex // Protects store access from background goroutine