fix(sqlite): add retry logic to transaction entry points (GH#1272)

Update withTx to use BEGIN IMMEDIATE with exponential backoff retry
on SQLITE_BUSY errors. This prevents "database is locked" failures
during concurrent operations (daemon + CLI, multi-agent workflows).

Changes:
- withTx now uses beginImmediateWithRetry (same pattern as RunInTransaction)
- Add dbExecutor interface for helper functions that work with both
  *sql.Tx and *sql.Conn
- Update all withTx callers to use *sql.Conn
- Refactor DeleteIssue to use withTx (fixes the specific error in auto-import)
- Update markIssuesDirtyTx to accept dbExecutor interface

Affected paths:
- MarkIssuesDirty, ClearDirtyIssuesByID (dirty.go)
- AddDependency, RemoveDependency (dependencies.go)
- executeLabelOperation (labels.go)
- AddComment (events.go)
- ApplyCompaction (compact.go)
- DeleteIssue (queries.go)

Note: Some direct BeginTx calls in queries.go (CloseIssue, UpdateIssue,
ReopenIssue, DeleteIssues) still use the old pattern and could be
refactored in a follow-up.

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

internal/storage/sqlite/dirty.go

@@ -31,9 +31,9 @@ func (s *SQLiteStorage) MarkIssuesDirty(ctx context.Context, issueIDs []string)
 		return nil
 	}
 
-	return s.withTx(ctx, func(tx *sql.Tx) error {
+	return s.withTx(ctx, func(conn *sql.Conn) error {
 		now := time.Now()
-		stmt, err := tx.PrepareContext(ctx, `
+		stmt, err := conn.PrepareContext(ctx, `
 			INSERT INTO dirty_issues (issue_id, marked_at)
 			VALUES (?, ?)
 			ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
@@ -117,8 +117,8 @@ func (s *SQLiteStorage) ClearDirtyIssuesByID(ctx context.Context, issueIDs []str
 		return nil
 	}
 
-	return s.withTx(ctx, func(tx *sql.Tx) error {
-		stmt, err := tx.PrepareContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`)
+	return s.withTx(ctx, func(conn *sql.Conn) error {
+		stmt, err := conn.PrepareContext(ctx, `DELETE FROM dirty_issues WHERE issue_id = ?`)
 		if err != nil {
 			return fmt.Errorf("failed to prepare statement: %w", err)
 		}
@@ -152,15 +152,16 @@ func (s *SQLiteStorage) GetDirtyIssueCount(ctx context.Context) (int, error) {
 	return count, nil
 }
 
-// markIssuesDirtyTx marks multiple issues as dirty within an existing transaction
-// This is a helper for operations that need to mark issues dirty as part of a larger transaction
-func markIssuesDirtyTx(ctx context.Context, tx *sql.Tx, issueIDs []string) error {
+// markIssuesDirtyTx marks multiple issues as dirty within an existing transaction.
+// This is a helper for operations that need to mark issues dirty as part of a larger transaction.
+// The exec parameter can be either *sql.Tx or *sql.Conn.
+func markIssuesDirtyTx(ctx context.Context, exec dbExecutor, issueIDs []string) error {
 	if len(issueIDs) == 0 {
 		return nil
 	}
 
 	now := time.Now()
-	stmt, err := tx.PrepareContext(ctx, `
+	stmt, err := exec.PrepareContext(ctx, `
 		INSERT INTO dirty_issues (issue_id, marked_at)
 		VALUES (?, ?)
 		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at