Fix ApplicationConfig format: preserve application: structure on round-trip, warn when sub-files unresolvable

src/components/WorkflowEditor.tsx

@@ -67,6 +67,14 @@ export function WorkflowEditor(props: WorkflowEditorProps) {
             'info',
           );
         }
+        // ApplicationConfig format detected but no file resolver provided — warn the user
+        // rather than silently converting the format.
+        if (config._applicationConfig && !onResolveFile) {
+          addToast(
+            'ApplicationConfig format detected. Configure a workspace file resolver to render the full application graph from referenced sub-files.',
+            'warning',
+          );
+        }
       }
       const mapFromProp = sourceMapProp ? new Map(Object.entries(sourceMapProp)) : undefined;
       importFromConfig(config, mapFromProp);

src/stores/workflowStore.ts

@@ -481,6 +481,11 @@ const useWorkflowStore = create<WorkflowStore>()(
     if (Object.keys(importedPipelines).length > 0) {
       config.pipelines = importedPipelines;
     }
+    // Reattach ApplicationConfig metadata so configToYaml / exportMainFileYaml
+    // can reconstruct the original `application:` format on export.
+    if (originalConfig?._applicationConfig) {
+      config._applicationConfig = originalConfig._applicationConfig;
+    }
     return config;
   },
 

src/types/workflow.ts

@@ -10,6 +10,18 @@ export interface ModuleConfig {
   ui_position?: { x: number; y: number };
 }
 
+/**
+ * Metadata preserved when a YAML file uses the ApplicationConfig format
+ * (`application:` top-level key with `workflows[].file` references).
+ * Stored alongside the merged WorkflowConfig so the original structure can be
+ * reconstructed on export without converting to the flat WorkflowConfig format.
+ */
+export interface ApplicationConfigMeta {
+  name?: string;
+  version?: string;
+  workflows: Array<{ file: string }>;
+}
+
 export interface WorkflowConfig {
   name?: string;
   version?: string;
@@ -23,6 +35,8 @@ export interface WorkflowConfig {
   infrastructure?: Record<string, unknown>;
   sidecars?: unknown[];
   _originalKeys?: string[];
+  /** Present when the source file used the ApplicationConfig format. */
+  _applicationConfig?: ApplicationConfigMeta;
   /** Preserves unknown top-level keys that are not part of the known schema (e.g. engine:, custom config blocks). */
   _extraTopLevelKeys?: Record<string, unknown>;
 }

src/utils/index.ts

@@ -12,6 +12,7 @@ export {
   exportToFiles,
   exportMainFileYaml,
   hasFileReferences,
+  buildApplicationConfigYaml,
 } from './serialization';
 export { layoutNodes } from './autoLayout';
 export {