Preserve unknown top-level YAML keys and fix metadata loss through import/export cycle

src/stores/workflowStore.ts

@@ -105,6 +105,15 @@ interface WorkflowStore {
   importedTriggers: Record<string, unknown>;
   importedPipelines: Record<string, unknown>;
 
+  /**
+   * Passthrough metadata from the most recently imported WorkflowConfig.
+   * Stores non-visual top-level fields (name, version, _originalKeys, _extraTopLevelKeys, imports,
+   * requires, platform, infrastructure, sidecars) so that exportToConfig() can reconstruct
+   * a complete WorkflowConfig without losing unknown keys or reformatting structure.
+   * Pipelines are excluded here because they are tracked separately via importedPipelines.
+   */
+  importedPassthrough: Omit<WorkflowConfig, 'modules' | 'workflows' | 'triggers' | 'pipelines'> | null;
+
   // Multi-file resolution: maps module name → source file path
   sourceMap: Map<string, string>;
   setSourceMap: (sourceMap: Map<string, string>) => void;
@@ -218,6 +227,7 @@ const useWorkflowStore = create<WorkflowStore>()(
   importedWorkflows: {},
   importedTriggers: {},
   importedPipelines: {},
+  importedPassthrough: null,
 
   // Multi-file resolution
   sourceMap: new Map<string, string>(),
@@ -453,9 +463,15 @@ const useWorkflowStore = create<WorkflowStore>()(
   },
 
   exportToConfig: () => {
-    const { nodes, edges, importedWorkflows, importedTriggers, importedPipelines } = get();
+    const { nodes, edges, importedWorkflows, importedTriggers, importedPipelines, importedPassthrough } = get();
     const moduleTypeMap = useModuleSchemaStore.getState().moduleTypeMap;
-    const config = nodesToConfig(nodes, edges, moduleTypeMap);
+    // Pass importedPassthrough as originalConfig so that nodesToConfig can restore
+    // non-visual fields: name, version, _originalKeys, _extraTopLevelKeys, imports,
+    // requires, platform, infrastructure, sidecars.
+    const originalConfig: import('../types/workflow.ts').WorkflowConfig | undefined = importedPassthrough
+      ? { modules: [], workflows: {}, triggers: {}, ...importedPassthrough }
+      : undefined;
+    const config = nodesToConfig(nodes, edges, moduleTypeMap, originalConfig);
     if (Object.keys(config.workflows).length === 0 && Object.keys(importedWorkflows).length > 0) {
       config.workflows = importedWorkflows;
     }
@@ -484,13 +500,17 @@ const useWorkflowStore = create<WorkflowStore>()(
     get().pushHistory();
     const moduleTypeMap = useModuleSchemaStore.getState().moduleTypeMap;
     const { nodes, edges } = configToNodes(config, moduleTypeMap, sourceMap);
+    // Extract passthrough metadata (everything except the visual module/workflow/trigger data)
+    const { modules: _modules, workflows: _workflows, triggers: _triggers, pipelines: _pipelines, ...passthroughFields } = config;
+    const importedPassthrough: WorkflowStore['importedPassthrough'] = passthroughFields;
     const updates: Partial<WorkflowStore> = {
       nodes,
       edges,
       selectedNodeId: null,
       importedWorkflows: config.workflows ?? {},
       importedTriggers: config.triggers ?? {},
       importedPipelines: config.pipelines ?? {},
+      importedPassthrough,
     };
     if (sourceMap) {
       updates.sourceMap = sourceMap;
@@ -501,7 +521,7 @@ const useWorkflowStore = create<WorkflowStore>()(
 
   clearCanvas: () => {
     get().pushHistory();
-    set({ nodes: [], edges: [], selectedNodeId: null, selectedEdgeId: null, nodeCounter: 0, importedWorkflows: {}, importedTriggers: {}, importedPipelines: {} });
+    set({ nodes: [], edges: [], selectedNodeId: null, selectedEdgeId: null, nodeCounter: 0, importedWorkflows: {}, importedTriggers: {}, importedPipelines: {}, importedPassthrough: null });
   },
 
   exportLayout: (): LayoutData => {

src/types/workflow.ts

@@ -23,6 +23,8 @@ export interface WorkflowConfig {
   infrastructure?: Record<string, unknown>;
   sidecars?: unknown[];
   _originalKeys?: string[];
+  /** Preserves unknown top-level keys that are not part of the known schema (e.g. engine:, custom config blocks). */
+  _extraTopLevelKeys?: Record<string, unknown>;
 }
 
 // Workflow section types for edge extraction

src/utils/serialization-bugs.test.ts

@@ -1,5 +1,5 @@
 import { describe, it, expect } from 'vitest';
-import { configToNodes, nodesToConfig, configToYaml, parseYamlSafe } from './serialization.ts';
+import { configToNodes, nodesToConfig, configToYaml, parseYamlSafe, parseYaml } from './serialization.ts';
 import { MODULE_TYPE_MAP } from '../types/workflow.ts';
 
 describe('Bug 1: name and version round-trip', () => {
@@ -136,3 +136,161 @@ triggers: {}
     expect(isPartial).toBe(false);
   });
 });
+
+describe('Bug 4: unknown top-level keys (e.g. engine:) must not be dropped', () => {
+  it('parseYaml captures unknown top-level keys in _extraTopLevelKeys', () => {
+    const yamlText = `
+name: my-service
+engine:
+  validation:
+    templateRefs: warn
+modules: []
+workflows: {}
+`;
+    const config = parseYaml(yamlText);
+    expect(config._extraTopLevelKeys).toBeDefined();
+    expect(config._extraTopLevelKeys!['engine']).toEqual({ validation: { templateRefs: 'warn' } });
+  });
+
+  it('parseYamlSafe captures unknown top-level keys in _extraTopLevelKeys', () => {
+    const yamlText = `
+name: my-service
+engine:
+  validation:
+    templateRefs: warn
+modules: []
+`;
+    const { config } = parseYamlSafe(yamlText);
+    expect(config._extraTopLevelKeys).toBeDefined();
+    expect(config._extraTopLevelKeys!['engine']).toEqual({ validation: { templateRefs: 'warn' } });
+  });
+
+  it('configToYaml emits unknown top-level keys', () => {
+    const yamlText = `
+name: my-service
+engine:
+  validation:
+    templateRefs: warn
+modules: []
+workflows: {}
+`;
+    const config = parseYaml(yamlText);
+    const out = configToYaml(config);
+    expect(out).toContain('engine:');
+    expect(out).toContain('templateRefs: warn');
+  });
+
+  it('nodesToConfig passes through _extraTopLevelKeys from originalConfig', () => {
+    const yamlText = `
+name: my-service
+engine:
+  validation:
+    templateRefs: warn
+modules:
+  - name: server
+    type: http.server
+    config:
+      address: ":8080"
+workflows: {}
+`;
+    const config = parseYaml(yamlText);
+    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
+    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
+    expect(exported._extraTopLevelKeys).toBeDefined();
+    expect(exported._extraTopLevelKeys!['engine']).toEqual({ validation: { templateRefs: 'warn' } });
+    const out = configToYaml(exported);
+    expect(out).toContain('engine:');
+  });
+
+  it('full round-trip preserves engine block and original key ordering', () => {
+    const yamlText = `name: my-service
+version: "1.0"
+engine:
+  validation:
+    templateRefs: warn
+modules:
+  - name: server
+    type: http.server
+    config:
+      address: ':8080'
+pipelines:
+  health:
+    trigger:
+      type: http
+      method: GET
+      path: /healthz
+`;
+    const config = parseYaml(yamlText);
+    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
+    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
+    const out = configToYaml(exported);
+
+    // engine block must be present
+    expect(out).toContain('engine:');
+    expect(out).toContain('templateRefs: warn');
+
+    // Key ordering: name comes before engine comes before modules
+    const nameIdx = out.indexOf('name:');
+    const engineIdx = out.indexOf('engine:');
+    const modulesIdx = out.indexOf('modules:');
+    expect(nameIdx).toBeGreaterThanOrEqual(0);
+    expect(engineIdx).toBeGreaterThan(nameIdx);
+    expect(modulesIdx).toBeGreaterThan(engineIdx);
+  });
+});
+
+describe('Bug 5: triggers: {} must not be injected when not in original', () => {
+  it('does not add triggers: {} when original YAML had no triggers key', () => {
+    const yamlText = `
+name: my-service
+modules:
+  - name: server
+    type: http.server
+    config:
+      address: ":8080"
+pipelines:
+  health:
+    trigger:
+      type: http
+      method: GET
+      path: /healthz
+`;
+    const config = parseYaml(yamlText);
+    // triggers not in original keys
+    expect(config._originalKeys).not.toContain('triggers');
+
+    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
+    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
+    const out = configToYaml(exported);
+
+    // triggers: {} must NOT appear in output
+    expect(out).not.toMatch(/^triggers:/m);
+  });
+});
+
+describe('Bug 6: parseYamlSafe is consistent with parseYaml for all fields', () => {
+  it('parseYamlSafe preserves imports, requires, platform, infrastructure, sidecars', () => {
+    const yamlText = `
+name: my-service
+imports:
+  - other.yaml
+requires:
+  some-service: ">=1.0"
+platform:
+  target: kubernetes
+infrastructure:
+  database:
+    type: postgres
+sidecars:
+  - name: proxy
+    image: envoy:latest
+modules: []
+`;
+    const { config } = parseYamlSafe(yamlText);
+    expect(config.imports).toEqual(['other.yaml']);
+    expect(config.requires).toEqual({ 'some-service': '>=1.0' });
+    expect(config.platform).toEqual({ target: 'kubernetes' });
+    expect(config.infrastructure).toEqual({ database: { type: 'postgres' } });
+    expect(config.sidecars).toHaveLength(1);
+  });
+});