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>

cmd/bd/export.go

@@ -83,9 +83,18 @@ Output to stdout by default, or use -o flag for file output.`,
 			}
 		}
 
-		// Clear auto-flush state since we just manually exported
-		// This cancels any pending auto-flush timer and marks DB as clean
-		clearAutoFlushState()
+		// Only clear dirty issues and auto-flush state if exporting to the default JSONL path
+		// This prevents clearing dirty flags when exporting to custom paths (e.g., bd export -o backup.jsonl)
+		if output == "" || output == findJSONLPath() {
+			// Clear dirty issues since we just exported to the canonical JSONL file
+			if err := store.ClearDirtyIssues(ctx); err != nil {
+				fmt.Fprintf(os.Stderr, "Warning: failed to clear dirty issues: %v\n", err)
+			}
+
+			// Clear auto-flush state since we just manually exported
+			// This cancels any pending auto-flush timer and marks DB as clean
+			clearAutoFlushState()
+		}
 	},
 }