fix: update tests to match stripped null/empty fields in MCP responses

- Expect undefined (not null/[]) for completedAt, subtasks, lastUsedAt, dependsOn
- Add explicit absence checks for mtime and mimeType
- Fix JSON.stringify replacer root-array bug (k !== '' guard) across search/list tools

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: prih

src/api/tools/knowledge/search-notes.ts

@@ -26,7 +26,7 @@ export function register(server: McpServer, mgr: KnowledgeGraphManager): void {
     },
     async ({ query, topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode }) => {
       const results = await mgr.searchNotes(query, { topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode });
-      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && Array.isArray(v) && v.length === 0 ? undefined : v);
       return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );

src/api/tools/skills/list-skills.ts

@@ -20,7 +20,7 @@ export function register(server: McpServer, mgr: SkillGraphManager): void {
     },
     async ({ source, tag, filter, limit }) => {
       const results = mgr.listSkills({ source, tag, filter, limit });
-      const clean = (_k: string, v: any) => (v === null || (Array.isArray(v) && v.length === 0) ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && (v === null || (Array.isArray(v) && v.length === 0)) ? undefined : v);
       const output = results.map(({ version: _, ...r }) => r);
       return { content: [{ type: 'text', text: JSON.stringify(output, clean, 2) }] };
     },

src/api/tools/skills/recall-skills.ts

@@ -19,7 +19,7 @@ export function register(server: McpServer, mgr: SkillGraphManager): void {
     },
     async ({ context, topK, minScore, searchMode }) => {
       const results = await mgr.searchSkills(context, { topK, minScore: minScore ?? 0.3, searchMode });
-      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && Array.isArray(v) && v.length === 0 ? undefined : v);
       return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );

src/api/tools/skills/search-skills.ts

@@ -26,7 +26,7 @@ export function register(server: McpServer, mgr: SkillGraphManager): void {
     },
     async ({ query, topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode }) => {
       const results = await mgr.searchSkills(query, { topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode });
-      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && Array.isArray(v) && v.length === 0 ? undefined : v);
       return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );

src/api/tools/tasks/list-tasks.ts

@@ -25,7 +25,7 @@ export function register(server: McpServer, mgr: TaskGraphManager): void {
     },
     async ({ status, priority, tag, filter, assignee, limit }) => {
       const results = mgr.listTasks({ status, priority, tag, filter, assignee, limit });
-      const clean = (_k: string, v: any) => (v === null || (Array.isArray(v) && v.length === 0) ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && (v === null || (Array.isArray(v) && v.length === 0)) ? undefined : v);
       const output = results.map(({ version: _, ...r }) => r);
       return { content: [{ type: 'text', text: JSON.stringify(output, clean, 2) }] };
     },

src/api/tools/tasks/search-tasks.ts

@@ -26,7 +26,7 @@ export function register(server: McpServer, mgr: TaskGraphManager): void {
     },
     async ({ query, topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode }) => {
       const results = await mgr.searchTasks(query, { topK, bfsDepth, maxResults, minScore, bfsDecay, searchMode });
-      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      const clean = (k: string, v: any) => (k !== '' && Array.isArray(v) && v.length === 0 ? undefined : v);
       return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );

src/tests/mcp-docs.test.ts

@@ -348,7 +348,7 @@ describe('MCP docs tools', () => {
       expect(typeof node.content).toBe('string');
       expect(node.content.length).toBeGreaterThan(0);
       expect(node.level).toBe(1);
-      expect(node.mtime).toBe(DOC_MTIME);
+      expect('mtime' in node).toBe(false);
       expect('embedding' in node).toBe(false);
     });
 

src/tests/mcp-file-index.test.ts

@@ -177,7 +177,7 @@ describe('files_get_info', () => {
     expect(info.fileName).toBe('config.ts');
     expect(info.extension).toBe('.ts');
     expect(info.language).toBe('typescript');
-    expect(info.mimeType).toBe('text/typescript');
+    expect('mimeType' in info).toBe(false);
     expect(info.size).toBe(1024);
     expect(info.directory).toBe('src/lib');
   });

src/tests/mcp-skills.test.ts

@@ -154,8 +154,8 @@ describe('MCP Skill Tools', () => {
       expect(skill.source).toBe('user');
       expect(skill.confidence).toBe(1);
       expect(skill.usageCount).toBe(0);
-      expect(skill.lastUsedAt).toBeNull();
-      expect(skill.dependsOn).toHaveLength(0);
+      expect(skill.lastUsedAt).toBeUndefined();
+      expect(skill.dependsOn).toBeUndefined();
     });
 
     it('skills_get returns error for missing', async () => {

src/tests/mcp-tasks.test.ts

@@ -125,7 +125,7 @@ describe('Task CRUD tools', () => {
     expect(task.status).toBe('backlog');
     expect(task.priority).toBe('high');
     expect(task.tags).toEqual(['bug', 'auth']);
-    expect(task.subtasks).toHaveLength(0);
+    expect(task.subtasks).toBeUndefined();
   });
 
   it('get_task returns error for missing', async () => {
@@ -159,7 +159,7 @@ describe('Task CRUD tools', () => {
     await call('tasks_update', { taskId: 'fix-auth-redirect', status: 'todo' });
     const task = json<TaskResult>(await call('tasks_get', { taskId: 'fix-auth-redirect' }));
     expect(task.status).toBe('todo');
-    expect(task.completedAt).toBeNull();
+    expect(task.completedAt).toBeUndefined();
   });
 
   // -- tasks_move --
@@ -170,7 +170,7 @@ describe('Task CRUD tools', () => {
       status: 'in_progress',
     }));
     expect(res.status).toBe('in_progress');
-    expect(res.completedAt).toBeNull();
+    expect(res.completedAt).toBeUndefined();
   });
 
   it('move_task to done sets completedAt', async () => {
@@ -187,7 +187,7 @@ describe('Task CRUD tools', () => {
       taskId: 'add-search-feature',
       status: 'todo',
     }));
-    expect(res.completedAt).toBeNull();
+    expect(res.completedAt).toBeUndefined();
   });
 
   // -- tasks_list --