Merge branch 'main' into win-defender-mitigation

# Conflicts:
#	.beads/issues.jsonl
#	README.md

cmd/bd/export.go

@@ -129,11 +129,26 @@ Output to stdout by default, or use -o flag for file output.`,
 
 		// Write JSONL
 		encoder := json.NewEncoder(out)
+		exportedIDs := make([]string, 0, len(issues))
 		for _, issue := range issues {
 			if err := encoder.Encode(issue); err != nil {
 				fmt.Fprintf(os.Stderr, "Error encoding issue %s: %v\n", issue.ID, err)
 				os.Exit(1)
 			}
+			exportedIDs = append(exportedIDs, issue.ID)
+		}
+
+		// 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 only the issues that were actually exported (fixes bd-52 race condition)
+			if err := store.ClearDirtyIssuesByID(ctx, exportedIDs); 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()
 		}
 
 		// If writing to file, atomically replace the target file