From 447f1360688180a134afdaaa610c7d7d23c12860 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 13:21:04 +0000
Subject: [PATCH 1/7] Initial plan


From 0928bc5143c9728e42ea6e265ea19b4dc2e10e60 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 13:33:35 +0000
Subject: [PATCH 2/7] Fix YAML reformatting: preserve unknown top-level keys,
 fix triggers injection, fix parseYamlSafe consistency

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/fdecd5e6-5e99-4497-be49-ba1ed4033a96

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/stores/workflowStore.ts          |  32 ++-
 src/types/workflow.ts                |   2 +
 src/utils/serialization-bugs.test.ts | 296 ++++++++++++++++++++++++++-
 src/utils/serialization.ts           | 109 ++++++++--
 4 files changed, 420 insertions(+), 19 deletions(-)

diff --git a/src/stores/workflowStore.ts b/src/stores/workflowStore.ts
index 2c57bd3..8586082 100644
--- a/src/stores/workflowStore.ts
+++ b/src/stores/workflowStore.ts
@@ -105,6 +105,14 @@ 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.
+   */
+  importedPassthrough: Omit<WorkflowConfig, 'modules' | 'workflows' | 'triggers'> | null;
+
   // Multi-file resolution: maps module name → source file path
   sourceMap: Map<string, string>;
   setSourceMap: (sourceMap: Map<string, string>) => void;
@@ -218,6 +226,7 @@ const useWorkflowStore = create<WorkflowStore>()(
   importedWorkflows: {},
   importedTriggers: {},
   importedPipelines: {},
+  importedPassthrough: null,
 
   // Multi-file resolution
   sourceMap: new Map<string, string>(),
@@ -453,9 +462,15 @@ 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;
     }
@@ -484,6 +499,18 @@ 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 importedPassthrough: WorkflowStore['importedPassthrough'] = {
+      ...(config.name !== undefined ? { name: config.name } : {}),
+      ...(config.version !== undefined ? { version: config.version } : {}),
+      ...(config._originalKeys ? { _originalKeys: config._originalKeys } : {}),
+      ...(config._extraTopLevelKeys ? { _extraTopLevelKeys: config._extraTopLevelKeys } : {}),
+      ...(config.imports ? { imports: config.imports } : {}),
+      ...(config.requires ? { requires: config.requires } : {}),
+      ...(config.platform ? { platform: config.platform } : {}),
+      ...(config.infrastructure ? { infrastructure: config.infrastructure } : {}),
+      ...(config.sidecars ? { sidecars: config.sidecars } : {}),
+    };
     const updates: Partial<WorkflowStore> = {
       nodes,
       edges,
@@ -491,6 +518,7 @@ const useWorkflowStore = create<WorkflowStore>()(
       importedWorkflows: config.workflows ?? {},
       importedTriggers: config.triggers ?? {},
       importedPipelines: config.pipelines ?? {},
+      importedPassthrough,
     };
     if (sourceMap) {
       updates.sourceMap = sourceMap;
diff --git a/src/types/workflow.ts b/src/types/workflow.ts
index 2b14df2..8fe68ea 100644
--- a/src/types/workflow.ts
+++ b/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
diff --git a/src/utils/serialization-bugs.test.ts b/src/utils/serialization-bugs.test.ts
index 92bd0fe..ed6ef83 100644
--- a/src/utils/serialization-bugs.test.ts
+++ b/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 +136,297 @@ 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);
+  });
+});
+
+
+describe('Bug 1: name and version round-trip', () => {
+  it('preserves name and version through parse → configToNodes → nodesToConfig', () => {
+    const yamlText = `
+name: my-app
+version: "1.0.0"
+modules:
+  - name: http-server
+    type: http.server
+    config:
+      port: 8080
+workflows:
+  http:
+    router: router
+    server: http-server
+    routes: []
+`;
+    const { config } = parseYamlSafe(yamlText);
+    expect(config.name).toBe('my-app');
+    expect(config.version).toBe('1.0.0');
+
+    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
+    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
+    expect(exported.name).toBe('my-app');
+    expect(exported.version).toBe('1.0.0');
+  });
+
+  it('preserves name and version in configToYaml output', () => {
+    const yamlText = `
+name: my-app
+version: "2.3.1"
+modules: []
+workflows: {}
+triggers: {}
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const out = configToYaml(config);
+    expect(out).toContain('name: my-app');
+    expect(out).toContain('version:');
+  });
+
+  it('does not emit name/version when not present', () => {
+    const yamlText = `
+modules: []
+workflows: {}
+triggers: {}
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const out = configToYaml(config);
+    expect(out).not.toContain('name:');
+    expect(out).not.toContain('version:');
+  });
+});
+
+describe('Bug 2: partial files do not get empty modules/workflows added', () => {
+  it('partial file with only pipelines does not get empty modules/workflows/triggers', () => {
+    const yamlText = `
+pipelines:
+  my-pipeline:
+    steps:
+      - name: greet
+        type: step.set
+        config:
+          values:
+            hello: world
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
+    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
+    const out = configToYaml(exported);
+    expect(out).not.toContain('modules:');
+    expect(out).not.toContain('workflows:');
+    expect(out).not.toContain('triggers:');
+    expect(out).toContain('pipelines:');
+  });
+
+  it('full config with modules/workflows/triggers preserves them even when empty', () => {
+    const yamlText = `
+modules: []
+workflows: {}
+triggers: {}
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const out = configToYaml(config);
+    expect(out).toContain('modules:');
+    expect(out).toContain('workflows:');
+    expect(out).toContain('triggers:');
+  });
+
+  it('config with non-empty modules always includes modules in output', () => {
+    const yamlText = `
+pipelines:
+  p: {}
+modules:
+  - name: s
+    type: http.server
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const out = configToYaml(config);
+    expect(out).toContain('modules:');
+  });
+});
+
+describe('Bug 3: partial config detection', () => {
+  it('detects partial config (pipelines only, no modules)', () => {
+    const yamlText = `
+pipelines:
+  test:
+    steps:
+      - name: s
+        type: step.set
+`;
+    const { config } = parseYamlSafe(yamlText);
+    expect(config.modules.length).toBe(0);
+    const isPartial =
+      config.modules.length === 0 &&
+      Object.keys(config.pipelines ?? {}).length > 0;
+    expect(isPartial).toBe(true);
+  });
+
+  it('does not flag full config as partial', () => {
+    const yamlText = `
+modules:
+  - name: s
+    type: http.server
+workflows: {}
+triggers: {}
+`;
+    const { config } = parseYamlSafe(yamlText);
+    const isPartial =
+      config.modules.length === 0 &&
+      Object.keys(config.pipelines ?? {}).length > 0;
+    expect(isPartial).toBe(false);
+  });
+});
diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index e0ed137..26da7d8 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -540,6 +540,9 @@ export function nodesToConfig(
   if (originalKeys) {
     result._originalKeys = originalKeys;
   }
+  if (originalConfig?._extraTopLevelKeys && Object.keys(originalConfig._extraTopLevelKeys).length > 0) {
+    result._extraTopLevelKeys = originalConfig._extraTopLevelKeys;
+  }
   return result;
 }
 
@@ -809,31 +812,76 @@ export function configToYaml(config: WorkflowConfig): string {
   // Strip internal tracking fields and omit empty top-level arrays/objects
   // that were not present in the original YAML
   const originalKeys = config._originalKeys;
-  const out: Record<string, unknown> = {};
-
-  // Field order: name, version, imports, requires, modules, workflows, triggers, pipelines, platform, infrastructure, sidecars
-  if (config.name !== undefined) out.name = config.name;
-  if (config.version !== undefined) out.version = config.version;
-  if (config.imports && config.imports.length > 0) out.imports = config.imports;
-  if (config.requires && Object.keys(config.requires).length > 0) out.requires = config.requires;
 
+  // Determine which known fields to include
   const includeModules = !originalKeys || originalKeys.includes('modules') || (config.modules?.length ?? 0) > 0;
-  if (includeModules && config.modules !== undefined) out.modules = config.modules;
-
   const includeWorkflows = !originalKeys || originalKeys.includes('workflows') || Object.keys(config.workflows ?? {}).length > 0;
-  if (includeWorkflows && config.workflows !== undefined) out.workflows = config.workflows;
-
   const includeTriggers = !originalKeys || originalKeys.includes('triggers') || Object.keys(config.triggers ?? {}).length > 0;
-  if (includeTriggers && config.triggers !== undefined) out.triggers = config.triggers;
 
-  if (config.pipelines && Object.keys(config.pipelines).length > 0) out.pipelines = config.pipelines;
-  if (config.platform && Object.keys(config.platform).length > 0) out.platform = config.platform;
-  if (config.infrastructure && Object.keys(config.infrastructure).length > 0) out.infrastructure = config.infrastructure;
-  if (config.sidecars && config.sidecars.length > 0) out.sidecars = config.sidecars;
+  // Build a map of all key→value pairs that should be emitted
+  const valueMap: Record<string, unknown> = {};
+  if (config.name !== undefined) valueMap.name = config.name;
+  if (config.version !== undefined) valueMap.version = config.version;
+  if (config.imports && config.imports.length > 0) valueMap.imports = config.imports;
+  if (config.requires && Object.keys(config.requires).length > 0) valueMap.requires = config.requires;
+  if (includeModules && config.modules !== undefined) valueMap.modules = config.modules;
+  if (includeWorkflows && config.workflows !== undefined) valueMap.workflows = config.workflows;
+  if (includeTriggers && config.triggers !== undefined) valueMap.triggers = config.triggers;
+  if (config.pipelines && Object.keys(config.pipelines).length > 0) valueMap.pipelines = config.pipelines;
+  if (config.platform && Object.keys(config.platform).length > 0) valueMap.platform = config.platform;
+  if (config.infrastructure && Object.keys(config.infrastructure).length > 0) valueMap.infrastructure = config.infrastructure;
+  if (config.sidecars && config.sidecars.length > 0) valueMap.sidecars = config.sidecars;
+  // Include any extra/unknown top-level keys (e.g. engine:, custom config blocks)
+  if (config._extraTopLevelKeys) {
+    for (const [k, v] of Object.entries(config._extraTopLevelKeys)) {
+      valueMap[k] = v;
+    }
+  }
+
+  // Build the output object — if we have the original key order, honour it so that
+  // the serialised YAML preserves the author's top-level key ordering.
+  const out: Record<string, unknown> = {};
+  if (originalKeys && originalKeys.length > 0) {
+    // First: emit keys in their original order
+    for (const key of originalKeys) {
+      if (key in valueMap) {
+        out[key] = valueMap[key];
+      }
+    }
+    // Then: emit any new keys that weren't in the original (e.g. added by the editor)
+    for (const [key, value] of Object.entries(valueMap)) {
+      if (!originalKeys.includes(key)) {
+        out[key] = value;
+      }
+    }
+  } else {
+    // No original key order — use the fixed default order:
+    // name, version, imports, requires, modules, workflows, triggers, pipelines, platform, infrastructure, sidecars, [extra]
+    for (const [key, value] of Object.entries(valueMap)) {
+      out[key] = value;
+    }
+  }
 
   return yaml.dump(out, { lineWidth: -1, noRefs: true, sortKeys: false });
 }
 
+/** Known top-level keys in WorkflowConfig — anything else is preserved as an extra key. */
+const KNOWN_TOP_LEVEL_KEYS = new Set([
+  'name', 'version', 'modules', 'workflows', 'triggers',
+  'pipelines', 'imports', 'requires', 'platform', 'infrastructure', 'sidecars',
+]);
+
+/** Extract unknown top-level keys from a parsed YAML object into _extraTopLevelKeys. */
+function extractExtraTopLevelKeys(parsed: Record<string, unknown>): Record<string, unknown> | undefined {
+  const extra: Record<string, unknown> = {};
+  for (const key of Object.keys(parsed)) {
+    if (!KNOWN_TOP_LEVEL_KEYS.has(key)) {
+      extra[key] = parsed[key];
+    }
+  }
+  return Object.keys(extra).length > 0 ? extra : undefined;
+}
+
 export function parseYaml(text: string): WorkflowConfig {
   try {
     const parsed = yaml.load(text) as Record<string, unknown>;
@@ -871,6 +919,10 @@ export function parseYaml(text: string): WorkflowConfig {
     if (parsed.sidecars) {
       config.sidecars = parsed.sidecars as unknown[];
     }
+    const extraTopLevelKeys = extractExtraTopLevelKeys(parsed);
+    if (extraTopLevelKeys) {
+      config._extraTopLevelKeys = extraTopLevelKeys;
+    }
     return config;
   } catch {
     return { modules: [], workflows: {}, triggers: {}, _originalKeys: [] };
@@ -899,6 +951,25 @@ export function parseYamlSafe(text: string): { config: WorkflowConfig; error?: s
     if (parsed.pipelines) {
       config.pipelines = parsed.pipelines as Record<string, unknown>;
     }
+    if (parsed.imports) {
+      config.imports = parsed.imports as string[];
+    }
+    if (parsed.requires) {
+      config.requires = parsed.requires as Record<string, unknown>;
+    }
+    if (parsed.platform) {
+      config.platform = parsed.platform as Record<string, unknown>;
+    }
+    if (parsed.infrastructure) {
+      config.infrastructure = parsed.infrastructure as Record<string, unknown>;
+    }
+    if (parsed.sidecars) {
+      config.sidecars = parsed.sidecars as unknown[];
+    }
+    const extraTopLevelKeys = extractExtraTopLevelKeys(parsed);
+    if (extraTopLevelKeys) {
+      config._extraTopLevelKeys = extraTopLevelKeys;
+    }
     return { config };
   } catch (e) {
     return { config: { modules: [], workflows: {}, triggers: {}, _originalKeys: [] }, error: (e as Error).message };
@@ -1187,6 +1258,12 @@ export async function resolveImports(
   const configVersion = (parsed.version ?? application?.version) as string | undefined;
   if (configName) config.name = configName;
   if (configVersion) config.version = configVersion;
+  // Preserve top-level key ordering and unknown keys from the main file
+  config._originalKeys = Object.keys(parsed);
+  const extraTopLevelKeys = extractExtraTopLevelKeys(parsed);
+  if (extraTopLevelKeys) {
+    config._extraTopLevelKeys = extraTopLevelKeys;
+  }
 
   return {
     config,

From 001b279e26197571290c79f5b4c49d0b0256b7d3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 13:39:23 +0000
Subject: [PATCH 3/7] Address code review: explicit extraTopLevelKeys null
 check, explicit default key ordering, simplified passthrough extraction

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/fdecd5e6-5e99-4497-be49-ba1ed4033a96

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/stores/workflowStore.ts          |  13 +--
 src/utils/serialization-bugs.test.ts | 136 ---------------------------
 src/utils/serialization.ts           |  16 +++-
 3 files changed, 15 insertions(+), 150 deletions(-)

diff --git a/src/stores/workflowStore.ts b/src/stores/workflowStore.ts
index 8586082..3a8ca08 100644
--- a/src/stores/workflowStore.ts
+++ b/src/stores/workflowStore.ts
@@ -500,17 +500,8 @@ const useWorkflowStore = create<WorkflowStore>()(
     const moduleTypeMap = useModuleSchemaStore.getState().moduleTypeMap;
     const { nodes, edges } = configToNodes(config, moduleTypeMap, sourceMap);
     // Extract passthrough metadata (everything except the visual module/workflow/trigger data)
-    const importedPassthrough: WorkflowStore['importedPassthrough'] = {
-      ...(config.name !== undefined ? { name: config.name } : {}),
-      ...(config.version !== undefined ? { version: config.version } : {}),
-      ...(config._originalKeys ? { _originalKeys: config._originalKeys } : {}),
-      ...(config._extraTopLevelKeys ? { _extraTopLevelKeys: config._extraTopLevelKeys } : {}),
-      ...(config.imports ? { imports: config.imports } : {}),
-      ...(config.requires ? { requires: config.requires } : {}),
-      ...(config.platform ? { platform: config.platform } : {}),
-      ...(config.infrastructure ? { infrastructure: config.infrastructure } : {}),
-      ...(config.sidecars ? { sidecars: config.sidecars } : {}),
-    };
+    const { modules: _m, workflows: _w, triggers: _t, pipelines: _p, ...passthroughFields } = config;
+    const importedPassthrough: WorkflowStore['importedPassthrough'] = passthroughFields;
     const updates: Partial<WorkflowStore> = {
       nodes,
       edges,
diff --git a/src/utils/serialization-bugs.test.ts b/src/utils/serialization-bugs.test.ts
index ed6ef83..5644e48 100644
--- a/src/utils/serialization-bugs.test.ts
+++ b/src/utils/serialization-bugs.test.ts
@@ -294,139 +294,3 @@ modules: []
     expect(config.sidecars).toHaveLength(1);
   });
 });
-
-
-describe('Bug 1: name and version round-trip', () => {
-  it('preserves name and version through parse → configToNodes → nodesToConfig', () => {
-    const yamlText = `
-name: my-app
-version: "1.0.0"
-modules:
-  - name: http-server
-    type: http.server
-    config:
-      port: 8080
-workflows:
-  http:
-    router: router
-    server: http-server
-    routes: []
-`;
-    const { config } = parseYamlSafe(yamlText);
-    expect(config.name).toBe('my-app');
-    expect(config.version).toBe('1.0.0');
-
-    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
-    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
-    expect(exported.name).toBe('my-app');
-    expect(exported.version).toBe('1.0.0');
-  });
-
-  it('preserves name and version in configToYaml output', () => {
-    const yamlText = `
-name: my-app
-version: "2.3.1"
-modules: []
-workflows: {}
-triggers: {}
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const out = configToYaml(config);
-    expect(out).toContain('name: my-app');
-    expect(out).toContain('version:');
-  });
-
-  it('does not emit name/version when not present', () => {
-    const yamlText = `
-modules: []
-workflows: {}
-triggers: {}
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const out = configToYaml(config);
-    expect(out).not.toContain('name:');
-    expect(out).not.toContain('version:');
-  });
-});
-
-describe('Bug 2: partial files do not get empty modules/workflows added', () => {
-  it('partial file with only pipelines does not get empty modules/workflows/triggers', () => {
-    const yamlText = `
-pipelines:
-  my-pipeline:
-    steps:
-      - name: greet
-        type: step.set
-        config:
-          values:
-            hello: world
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const { nodes, edges } = configToNodes(config, MODULE_TYPE_MAP);
-    const exported = nodesToConfig(nodes, edges, MODULE_TYPE_MAP, config);
-    const out = configToYaml(exported);
-    expect(out).not.toContain('modules:');
-    expect(out).not.toContain('workflows:');
-    expect(out).not.toContain('triggers:');
-    expect(out).toContain('pipelines:');
-  });
-
-  it('full config with modules/workflows/triggers preserves them even when empty', () => {
-    const yamlText = `
-modules: []
-workflows: {}
-triggers: {}
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const out = configToYaml(config);
-    expect(out).toContain('modules:');
-    expect(out).toContain('workflows:');
-    expect(out).toContain('triggers:');
-  });
-
-  it('config with non-empty modules always includes modules in output', () => {
-    const yamlText = `
-pipelines:
-  p: {}
-modules:
-  - name: s
-    type: http.server
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const out = configToYaml(config);
-    expect(out).toContain('modules:');
-  });
-});
-
-describe('Bug 3: partial config detection', () => {
-  it('detects partial config (pipelines only, no modules)', () => {
-    const yamlText = `
-pipelines:
-  test:
-    steps:
-      - name: s
-        type: step.set
-`;
-    const { config } = parseYamlSafe(yamlText);
-    expect(config.modules.length).toBe(0);
-    const isPartial =
-      config.modules.length === 0 &&
-      Object.keys(config.pipelines ?? {}).length > 0;
-    expect(isPartial).toBe(true);
-  });
-
-  it('does not flag full config as partial', () => {
-    const yamlText = `
-modules:
-  - name: s
-    type: http.server
-workflows: {}
-triggers: {}
-`;
-    const { config } = parseYamlSafe(yamlText);
-    const isPartial =
-      config.modules.length === 0 &&
-      Object.keys(config.pipelines ?? {}).length > 0;
-    expect(isPartial).toBe(false);
-  });
-});
diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index 26da7d8..3d7da59 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -540,8 +540,9 @@ export function nodesToConfig(
   if (originalKeys) {
     result._originalKeys = originalKeys;
   }
-  if (originalConfig?._extraTopLevelKeys && Object.keys(originalConfig._extraTopLevelKeys).length > 0) {
-    result._extraTopLevelKeys = originalConfig._extraTopLevelKeys;
+  const extraTopLevelKeys = originalConfig?._extraTopLevelKeys;
+  if (extraTopLevelKeys && Object.keys(extraTopLevelKeys).length > 0) {
+    result._extraTopLevelKeys = extraTopLevelKeys;
   }
   return result;
 }
@@ -857,8 +858,17 @@ export function configToYaml(config: WorkflowConfig): string {
   } else {
     // No original key order — use the fixed default order:
     // name, version, imports, requires, modules, workflows, triggers, pipelines, platform, infrastructure, sidecars, [extra]
+    const DEFAULT_ORDER = ['name', 'version', 'imports', 'requires', 'modules', 'workflows', 'triggers', 'pipelines', 'platform', 'infrastructure', 'sidecars'];
+    for (const key of DEFAULT_ORDER) {
+      if (key in valueMap) {
+        out[key] = valueMap[key];
+      }
+    }
+    // Append any extra top-level keys after the known fields
     for (const [key, value] of Object.entries(valueMap)) {
-      out[key] = value;
+      if (!DEFAULT_ORDER.includes(key)) {
+        out[key] = value;
+      }
     }
   }
 

From 1f14b2b110f56074037d23832a48f8483c861119 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 13:41:37 +0000
Subject: [PATCH 4/7] Address code review: move KNOWN_TOP_LEVEL_KEYS before
 configToYaml, use clearer destructuring names

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/fdecd5e6-5e99-4497-be49-ba1ed4033a96

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/stores/workflowStore.ts |  2 +-
 src/utils/serialization.ts  | 34 +++++++++++++++++-----------------
 2 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/src/stores/workflowStore.ts b/src/stores/workflowStore.ts
index 3a8ca08..7fd99cb 100644
--- a/src/stores/workflowStore.ts
+++ b/src/stores/workflowStore.ts
@@ -500,7 +500,7 @@ const useWorkflowStore = create<WorkflowStore>()(
     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: _m, workflows: _w, triggers: _t, pipelines: _p, ...passthroughFields } = config;
+    const { modules: _modules, workflows: _workflows, triggers: _triggers, pipelines: _pipelines, ...passthroughFields } = config;
     const importedPassthrough: WorkflowStore['importedPassthrough'] = passthroughFields;
     const updates: Partial<WorkflowStore> = {
       nodes,
diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index 3d7da59..ad41272 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -809,6 +809,23 @@ export function nodeComponentType(moduleType: string): string {
   return 'infrastructureNode';
 }
 
+/** Known top-level keys in WorkflowConfig — anything else is preserved as an extra key. */
+const KNOWN_TOP_LEVEL_KEYS = new Set([
+  'name', 'version', 'modules', 'workflows', 'triggers',
+  'pipelines', 'imports', 'requires', 'platform', 'infrastructure', 'sidecars',
+]);
+
+/** Extract unknown top-level keys from a parsed YAML object into _extraTopLevelKeys. */
+function extractExtraTopLevelKeys(parsed: Record<string, unknown>): Record<string, unknown> | undefined {
+  const extra: Record<string, unknown> = {};
+  for (const key of Object.keys(parsed)) {
+    if (!KNOWN_TOP_LEVEL_KEYS.has(key)) {
+      extra[key] = parsed[key];
+    }
+  }
+  return Object.keys(extra).length > 0 ? extra : undefined;
+}
+
 export function configToYaml(config: WorkflowConfig): string {
   // Strip internal tracking fields and omit empty top-level arrays/objects
   // that were not present in the original YAML
@@ -875,23 +892,6 @@ export function configToYaml(config: WorkflowConfig): string {
   return yaml.dump(out, { lineWidth: -1, noRefs: true, sortKeys: false });
 }
 
-/** Known top-level keys in WorkflowConfig — anything else is preserved as an extra key. */
-const KNOWN_TOP_LEVEL_KEYS = new Set([
-  'name', 'version', 'modules', 'workflows', 'triggers',
-  'pipelines', 'imports', 'requires', 'platform', 'infrastructure', 'sidecars',
-]);
-
-/** Extract unknown top-level keys from a parsed YAML object into _extraTopLevelKeys. */
-function extractExtraTopLevelKeys(parsed: Record<string, unknown>): Record<string, unknown> | undefined {
-  const extra: Record<string, unknown> = {};
-  for (const key of Object.keys(parsed)) {
-    if (!KNOWN_TOP_LEVEL_KEYS.has(key)) {
-      extra[key] = parsed[key];
-    }
-  }
-  return Object.keys(extra).length > 0 ? extra : undefined;
-}
-
 export function parseYaml(text: string): WorkflowConfig {
   try {
     const parsed = yaml.load(text) as Record<string, unknown>;

From 917109ec5086dc3404547144b7637f149ce7254b Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 14:16:36 +0000
Subject: [PATCH 5/7] Fix review feedback: clearCanvas resets
 importedPassthrough, exclude pipelines from passthrough type, fix
 buildMainFileContent for multi-file key ordering and unknown keys

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/cbe50c21-b5cc-4238-ab7b-36cb53bc6e40

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/stores/workflowStore.ts |  5 ++--
 src/utils/serialization.ts  | 47 +++++++++++++++++++++++--------------
 2 files changed, 33 insertions(+), 19 deletions(-)

diff --git a/src/stores/workflowStore.ts b/src/stores/workflowStore.ts
index 7fd99cb..0bdaef9 100644
--- a/src/stores/workflowStore.ts
+++ b/src/stores/workflowStore.ts
@@ -110,8 +110,9 @@ interface WorkflowStore {
    * 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'> | null;
+  importedPassthrough: Omit<WorkflowConfig, 'modules' | 'workflows' | 'triggers' | 'pipelines'> | null;
 
   // Multi-file resolution: maps module name → source file path
   sourceMap: Map<string, string>;
@@ -520,7 +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 => {
diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index ad41272..c01f242 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -813,6 +813,8 @@ export function nodeComponentType(moduleType: string): string {
 const KNOWN_TOP_LEVEL_KEYS = new Set([
   'name', 'version', 'modules', 'workflows', 'triggers',
   'pipelines', 'imports', 'requires', 'platform', 'infrastructure', 'sidecars',
+  // application: is the legacy multi-file format key — handled by resolveImports, not a passthrough extra
+  'application',
 ]);
 
 /** Extract unknown top-level keys from a parsed YAML object into _extraTopLevelKeys. */
@@ -1361,6 +1363,8 @@ export function exportMainFileYaml(
 
 /**
  * Internal helper: build the main-file YAML string and collect imported file paths.
+ * Delegates to configToYaml so that _extraTopLevelKeys and _originalKeys ordering
+ * are honoured for the main-file content (same as single-file round-trips).
  */
 function buildMainFileContent(
   config: WorkflowConfig,
@@ -1368,20 +1372,7 @@ function buildMainFileContent(
   filePipelines: Map<string | null, Record<string, unknown>>,
 ): { yaml: string; importedFiles: string[] } {
   const mainModules = fileModules.get(null) ?? [];
-  const mainConfig: Record<string, unknown> = {};
-  if (config.name !== undefined) mainConfig.name = config.name;
-  if (config.version !== undefined) mainConfig.version = config.version;
-  mainConfig.modules = mainModules;
-  if (Object.keys(config.workflows).length > 0) {
-    mainConfig.workflows = config.workflows;
-  }
-  if (Object.keys(config.triggers).length > 0) {
-    mainConfig.triggers = config.triggers;
-  }
   const mainPipelines = filePipelines.get(null);
-  if (mainPipelines && Object.keys(mainPipelines).length > 0) {
-    mainConfig.pipelines = mainPipelines;
-  }
 
   // Collect all non-null file paths across modules and pipelines
   const importedFiles = [
@@ -1390,11 +1381,33 @@ function buildMainFileContent(
       ...[...filePipelines.keys()].filter((k) => k !== null),
     ]),
   ] as string[];
-  if (importedFiles.length > 0) {
-    mainConfig.imports = importedFiles;
-  }
 
-  return { yaml: yaml.dump(mainConfig, { lineWidth: -1, noRefs: true, sortKeys: false }), importedFiles };
+  // For multi-file main files, ensure 'modules' is in _originalKeys so configToYaml
+  // always includes the modules section (even if empty, since sub-files provide modules
+  // via imports:). Without this, configs whose original main file had no top-level
+  // 'modules:' key (e.g. application: format) would omit modules from the export.
+  const computedOriginalKeys = config._originalKeys
+    ? (config._originalKeys.includes('modules')
+        ? config._originalKeys
+        : [...config._originalKeys, 'modules'])
+    : undefined;
+
+  // Build a temporary config that represents only the main-file content.
+  // By reusing the full config (with its _originalKeys, _extraTopLevelKeys, workflows,
+  // triggers, name, version, etc.) but substituting the main-file-only modules, pipelines,
+  // and the dynamically computed imports list, we can delegate to configToYaml and get
+  // correct key ordering and unknown-key preservation for free.
+  const mainOnlyConfig: WorkflowConfig = {
+    ...config,
+    modules: mainModules,
+    // Override imports with the computed list of imported file paths
+    imports: importedFiles.length > 0 ? importedFiles : undefined,
+    // Only include main-file pipelines
+    pipelines: mainPipelines && Object.keys(mainPipelines).length > 0 ? mainPipelines : undefined,
+    _originalKeys: computedOriginalKeys,
+  };
+
+  return { yaml: configToYaml(mainOnlyConfig), importedFiles };
 }
 
 /**

From fc9c9c714caad5f60745f7914eb48e87cfc8fd98 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 14:18:59 +0000
Subject: [PATCH 6/7] Refactor nested ternary in buildMainFileContent to
 if-else for clarity

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/cbe50c21-b5cc-4238-ab7b-36cb53bc6e40

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/utils/serialization.ts | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index c01f242..4bcfb4e 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -1386,11 +1386,10 @@ function buildMainFileContent(
   // always includes the modules section (even if empty, since sub-files provide modules
   // via imports:). Without this, configs whose original main file had no top-level
   // 'modules:' key (e.g. application: format) would omit modules from the export.
-  const computedOriginalKeys = config._originalKeys
-    ? (config._originalKeys.includes('modules')
-        ? config._originalKeys
-        : [...config._originalKeys, 'modules'])
-    : undefined;
+  let computedOriginalKeys = config._originalKeys;
+  if (computedOriginalKeys && !computedOriginalKeys.includes('modules')) {
+    computedOriginalKeys = [...computedOriginalKeys, 'modules'];
+  }
 
   // Build a temporary config that represents only the main-file content.
   // By reusing the full config (with its _originalKeys, _extraTopLevelKeys, workflows,

From 6c5ce0e8be531517422ab0d2e0a98c45a4531478 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Wed, 8 Apr 2026 14:21:06 +0000
Subject: [PATCH 7/7] Style: use adjustedOriginalKeys and conditional spread
 for imports in buildMainFileContent

Agent-Logs-Url: https://github.com/GoCodeAlone/workflow-editor/sessions/cbe50c21-b5cc-4238-ab7b-36cb53bc6e40

Co-authored-by: intel352 <77607+intel352@users.noreply.github.com>
---
 src/utils/serialization.ts | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/src/utils/serialization.ts b/src/utils/serialization.ts
index 4bcfb4e..f209c4d 100644
--- a/src/utils/serialization.ts
+++ b/src/utils/serialization.ts
@@ -1386,10 +1386,11 @@ function buildMainFileContent(
   // always includes the modules section (even if empty, since sub-files provide modules
   // via imports:). Without this, configs whose original main file had no top-level
   // 'modules:' key (e.g. application: format) would omit modules from the export.
-  let computedOriginalKeys = config._originalKeys;
-  if (computedOriginalKeys && !computedOriginalKeys.includes('modules')) {
-    computedOriginalKeys = [...computedOriginalKeys, 'modules'];
-  }
+  const sourceKeys = config._originalKeys;
+  const adjustedOriginalKeys =
+    sourceKeys && !sourceKeys.includes('modules')
+      ? [...sourceKeys, 'modules']
+      : sourceKeys;
 
   // Build a temporary config that represents only the main-file content.
   // By reusing the full config (with its _originalKeys, _extraTopLevelKeys, workflows,
@@ -1399,11 +1400,12 @@ function buildMainFileContent(
   const mainOnlyConfig: WorkflowConfig = {
     ...config,
     modules: mainModules,
-    // Override imports with the computed list of imported file paths
-    imports: importedFiles.length > 0 ? importedFiles : undefined,
+    // Override imports with the computed list of imported file paths (omit the property
+    // entirely when there are no sub-files so configToYaml does not emit `imports: []`)
+    ...(importedFiles.length > 0 ? { imports: importedFiles } : { imports: undefined }),
     // Only include main-file pipelines
     pipelines: mainPipelines && Object.keys(mainPipelines).length > 0 ? mainPipelines : undefined,
-    _originalKeys: computedOriginalKeys,
+    _originalKeys: adjustedOriginalKeys,
   };
 
   return { yaml: configToYaml(mainOnlyConfig), importedFiles };