Refactor: Replace manual transaction handling with withTx() helper

Fixes bd-1b0a

Changes:
- Added withTx() helper in util.go for cleaner transaction handling
- Kept ExecInTransaction() as deprecated wrapper for backward compatibility
- Refactored all manual BEGIN/COMMIT/ROLLBACK blocks to use withTx():
  - events.go: AddComment
  - dirty.go: MarkIssuesDirty, ClearDirtyIssuesByID
  - labels.go: executeLabelOperation
  - dependencies.go: AddDependency, RemoveDependency
  - compact.go: ApplyCompaction

All tests pass.

Amp-Thread-ID: https://ampcode.com/threads/T-dfacc972-f6c8-4bb3-8997-faa079b5d070
Co-authored-by: Amp <amp@ampcode.com>

internal/storage/sqlite/util.go

@@ -18,10 +18,10 @@ func (s *SQLiteStorage) BeginTx(ctx context.Context) (*sql.Tx, error) {
 	return s.db.BeginTx(ctx, nil)
 }
 
-// ExecInTransaction executes a function within a database transaction.
+// withTx executes a function within a database transaction.
 // If the function returns an error, the transaction is rolled back.
 // Otherwise, the transaction is committed.
-func (s *SQLiteStorage) ExecInTransaction(ctx context.Context, fn func(*sql.Tx) error) error {
+func (s *SQLiteStorage) withTx(ctx context.Context, fn func(*sql.Tx) error) error {
 	tx, err := s.db.BeginTx(ctx, nil)
 	if err != nil {
 		return fmt.Errorf("failed to begin transaction: %w", err)
@@ -39,6 +39,11 @@ func (s *SQLiteStorage) ExecInTransaction(ctx context.Context, fn func(*sql.Tx)
 	return nil
 }
 
+// ExecInTransaction is deprecated. Use withTx instead.
+func (s *SQLiteStorage) ExecInTransaction(ctx context.Context, fn func(*sql.Tx) error) error {
+	return s.withTx(ctx, fn)
+}
+
 // IsUniqueConstraintError checks if an error is a UNIQUE constraint violation
 func IsUniqueConstraintError(err error) bool {
 	if err == nil {