feat: add bd doctor check for orphaned issues (bd-5hrq)

- Add CheckOrphanedIssues to detect issues referenced in commits but still open
- Pattern matches (prefix-xxx) in git log against open issues in database
- Reports warning with issue IDs and commit hashes
- Add 8 comprehensive tests for the new check

Also:
- Add tests for mol spawn --attach functionality (bd-f7p1)
- Document commit message convention in AGENT_INSTRUCTIONS.md
- Fix CheckpointWAL to use wrapDBError for consistency

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

internal/storage/sqlite/store.go

@@ -344,7 +344,7 @@ func (s *SQLiteStorage) UnderlyingConn(ctx context.Context) (*sql.Conn, error) {
 // - Makes database safe for backup/copy operations
 func (s *SQLiteStorage) CheckpointWAL(ctx context.Context) error {
 	_, err := s.db.ExecContext(ctx, "PRAGMA wal_checkpoint(FULL)")
-	return err
+	return wrapDBError("checkpoint WAL", err)
 }
 
 // EnableFreshnessChecking enables detection of external database file modifications.