Implement incremental JSONL export with dirty issue tracking

Optimize auto-flush by tracking which issues have changed instead of
exporting the entire database on every flush. For large projects with
1000+ issues, this provides significant performance improvements.

Changes:
- Add dirty_issues table to schema with issue_id and marked_at columns
- Implement dirty tracking functions in new dirty.go file:
  * MarkIssueDirty() - Mark single issue as needing export
  * MarkIssuesDirty() - Batch mark multiple issues efficiently
  * GetDirtyIssues() - Query which issues need export
  * ClearDirtyIssues() - Clear tracking after successful export
  * GetDirtyIssueCount() - Monitor dirty issue count
- Update all CRUD operations to mark affected issues as dirty:
  * CreateIssue, UpdateIssue, DeleteIssue
  * AddDependency, RemoveDependency (marks both issues)
  * AddLabel, RemoveLabel, AddEvent
- Modify export to support incremental mode:
  * Add --incremental flag to export only dirty issues
  * Used by auto-flush for performance
  * Full export still available without flag
- Add Storage interface methods for dirty tracking

Performance impact: With incremental export, large databases only write
changed issues instead of regenerating entire JSONL file on every
auto-flush.

Closes bd-39

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

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

internal/storage/sqlite/dependencies.go

@@ -110,6 +110,26 @@ func (s *SQLiteStorage) AddDependency(ctx context.Context, dep *types.Dependency
 		return fmt.Errorf("failed to record event: %w", err)
 	}
 
+	// Mark both issues as dirty for incremental export
+	// (dependencies are exported with each issue, so both need updating)
+	now := time.Now()
+	stmt, err := tx.PrepareContext(ctx, `
+		INSERT INTO dirty_issues (issue_id, marked_at)
+		VALUES (?, ?)
+		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to prepare dirty statement: %w", err)
+	}
+	defer stmt.Close()
+
+	if _, err := stmt.ExecContext(ctx, dep.IssueID, now); err != nil {
+		return fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+	if _, err := stmt.ExecContext(ctx, dep.DependsOnID, now); err != nil {
+		return fmt.Errorf("failed to mark dependency target dirty: %w", err)
+	}
+
 	return tx.Commit()
 }
 
@@ -137,6 +157,25 @@ func (s *SQLiteStorage) RemoveDependency(ctx context.Context, issueID, dependsOn
 		return fmt.Errorf("failed to record event: %w", err)
 	}
 
+	// Mark both issues as dirty for incremental export
+	now := time.Now()
+	stmt, err := tx.PrepareContext(ctx, `
+		INSERT INTO dirty_issues (issue_id, marked_at)
+		VALUES (?, ?)
+		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to prepare dirty statement: %w", err)
+	}
+	defer stmt.Close()
+
+	if _, err := stmt.ExecContext(ctx, issueID, now); err != nil {
+		return fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+	if _, err := stmt.ExecContext(ctx, dependsOnID, now); err != nil {
+		return fmt.Errorf("failed to mark dependency target dirty: %w", err)
+	}
+
 	return tx.Commit()
 }