fix(storage): add reconnectMu RLock protection to prevent race condition (#1054)

Add missing reconnectMu.RLock() protection to storage methods that were
vulnerable to the same race condition fixed in GH#607. The FreshnessChecker
can trigger reconnect() which closes s.db while queries are in flight,
causing "database is closed" errors during daemon export operations.

Protected methods:
- labels.go: GetLabelsForIssues (GetLabels intentionally unprotected - called from GetIssue which holds lock)
- comments.go: GetIssueComments, GetCommentsForIssues
- dependencies.go: GetDependencyCounts, GetDependencyRecords, GetAllDependencyRecords, GetDependencyTree, loadDependencyGraph
- config.go: SetConfig, GetConfig, GetAllConfig, DeleteConfig, SetMetadata, GetMetadata
- dirty.go: MarkIssueDirty, GetDirtyIssues, GetDirtyIssueHash, GetDirtyIssueCount
- events.go: GetEvents, GetStatistics, GetMoleculeProgress
- hash.go: All hash methods
- hash_ids.go: GetNextChildID, ensureChildCounterUpdated (getNextChildNumber unprotected - called internally)

Internal helpers called from already-locked contexts intentionally omit
RLock to avoid deadlock (Go's RWMutex doesn't support recursive locking).

Fixes: bd-vx7fp

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

Executed-By: beads/crew/dave
Rig: beads
Role: crew

internal/storage/sqlite/dirty.go

@@ -11,6 +11,11 @@ import (
 // MarkIssueDirty marks an issue as dirty (needs to be exported to JSONL)
 // This should be called whenever an issue is created, updated, or has dependencies changed
 func (s *SQLiteStorage) MarkIssueDirty(ctx context.Context, issueID string) error {
+	// Hold read lock during database operations to prevent reconnect() from
+	// closing the connection mid-query (GH#607 race condition fix)
+	s.reconnectMu.RLock()
+	defer s.reconnectMu.RUnlock()
+
 	_, err := s.db.ExecContext(ctx, `
 		INSERT INTO dirty_issues (issue_id, marked_at)
 		VALUES (?, ?)
@@ -50,6 +55,11 @@ func (s *SQLiteStorage) MarkIssuesDirty(ctx context.Context, issueIDs []string)
 
 // GetDirtyIssues returns the list of issue IDs that need to be exported
 func (s *SQLiteStorage) GetDirtyIssues(ctx context.Context) ([]string, error) {
+	// Hold read lock during database operations to prevent reconnect() from
+	// closing the connection mid-query (GH#607 race condition fix)
+	s.reconnectMu.RLock()
+	defer s.reconnectMu.RUnlock()
+
 	rows, err := s.db.QueryContext(ctx, `
 		SELECT issue_id FROM dirty_issues
 		ORDER BY marked_at ASC
@@ -76,6 +86,11 @@ func (s *SQLiteStorage) GetDirtyIssues(ctx context.Context) ([]string, error) {
 
 // GetDirtyIssueHash returns the stored content hash for a dirty issue, if it exists
 func (s *SQLiteStorage) GetDirtyIssueHash(ctx context.Context, issueID string) (string, error) {
+	// Hold read lock during database operations to prevent reconnect() from
+	// closing the connection mid-query (GH#607 race condition fix)
+	s.reconnectMu.RLock()
+	defer s.reconnectMu.RUnlock()
+
 	var hash sql.NullString
 	err := s.db.QueryRowContext(ctx, `
 		SELECT content_hash FROM dirty_issues WHERE issue_id = ?
@@ -121,6 +136,11 @@ func (s *SQLiteStorage) ClearDirtyIssuesByID(ctx context.Context, issueIDs []str
 
 // GetDirtyIssueCount returns the count of dirty issues (for monitoring/debugging)
 func (s *SQLiteStorage) GetDirtyIssueCount(ctx context.Context) (int, error) {
+	// Hold read lock during database operations to prevent reconnect() from
+	// closing the connection mid-query (GH#607 race condition fix)
+	s.reconnectMu.RLock()
+	defer s.reconnectMu.RUnlock()
+
 	var count int
 	err := s.db.QueryRowContext(ctx, `SELECT COUNT(*) FROM dirty_issues`).Scan(&count)
 	if IsNotFound(wrapDBError("count dirty issues", err)) {