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/events.go

@@ -4,13 +4,20 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"time"
 
 	"github.com/steveyegge/beads/internal/types"
 )
 
 // AddComment adds a comment to an issue
 func (s *SQLiteStorage) AddComment(ctx context.Context, issueID, actor, comment string) error {
-	_, err := s.db.ExecContext(ctx, `
+	tx, err := s.db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction: %w", err)
+	}
+	defer tx.Rollback()
+
+	_, err = tx.ExecContext(ctx, `
 		INSERT INTO events (issue_id, event_type, actor, comment)
 		VALUES (?, ?, ?, ?)
 	`, issueID, types.EventCommented, actor, comment)
@@ -19,14 +26,25 @@ func (s *SQLiteStorage) AddComment(ctx context.Context, issueID, actor, comment
 	}
 
 	// Update issue updated_at timestamp
-	_, err = s.db.ExecContext(ctx, `
-		UPDATE issues SET updated_at = CURRENT_TIMESTAMP WHERE id = ?
-	`, issueID)
+	now := time.Now()
+	_, err = tx.ExecContext(ctx, `
+		UPDATE issues SET updated_at = ? WHERE id = ?
+	`, now, issueID)
 	if err != nil {
 		return fmt.Errorf("failed to update timestamp: %w", err)
 	}
 
-	return nil
+	// Mark issue as dirty for incremental export
+	_, err = tx.ExecContext(ctx, `
+		INSERT INTO dirty_issues (issue_id, marked_at)
+		VALUES (?, ?)
+		ON CONFLICT (issue_id) DO UPDATE SET marked_at = excluded.marked_at
+	`, issueID, now)
+	if err != nil {
+		return fmt.Errorf("failed to mark issue dirty: %w", err)
+	}
+
+	return tx.Commit()
 }
 
 // GetEvents returns the event history for an issue