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>

internal/storage/sqlite/util.go

@@ -8,7 +8,6 @@ import (
 )
 
 // QueryContext exposes the underlying database QueryContext method for advanced queries
-// This is used by commands that need direct SQL access (e.g., bd stale)
 func (s *SQLiteStorage) QueryContext(ctx context.Context, query string, args ...interface{}) (*sql.Rows, error) {
 	return s.db.QueryContext(ctx, query, args...)
 }