fix: strip empty arrays and nulls from remaining MCP tool responses

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

Author: prih

src/api/tools/docs/explain-symbol.ts

@@ -54,7 +54,8 @@ export function register(server: McpServer, mgr: DocGraphManager): void {
         return { content: [{ type: 'text', text: `No documentation found for symbol: ${symbol}` }] };
       }
 
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (v === null || (Array.isArray(v) && v.length === 0) ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/docs/list-snippets.ts

@@ -53,7 +53,8 @@ export function register(server: McpServer, mgr: DocGraphManager): void {
         return { content: [{ type: 'text', text: 'No code snippets found matching the criteria.' }] };
       }
 
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/file-index/search-all-files.ts

@@ -24,7 +24,8 @@ export function register(server: McpServer, mgr: FileIndexGraphManager): void {
     },
     async ({ query, limit = FILE_SEARCH_TOP_K, minScore = SEARCH_MIN_SCORE_FILES }) => {
       const results = await mgr.search(query, { topK: limit, minScore });
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (v === null ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/knowledge/find-linked-notes.ts

@@ -25,7 +25,8 @@ export function register(server: McpServer, mgr: KnowledgeGraphManager): void {
       if (results.length === 0) {
         return { content: [{ type: 'text', text: `No notes linked to ${targetGraph}::${targetId}` }] };
       }
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

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

@@ -26,7 +26,8 @@ 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 });
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/skills/find-linked-skills.ts

@@ -25,7 +25,8 @@ export function register(server: McpServer, mgr: SkillGraphManager): void {
       if (results.length === 0) {
         return { content: [{ type: 'text', text: `No skills linked to ${targetGraph}::${targetId}` }] };
       }
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

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

@@ -19,7 +19,8 @@ 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 });
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (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 +26,8 @@ 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 });
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/tasks/find-linked-tasks.ts

@@ -25,7 +25,8 @@ export function register(server: McpServer, mgr: TaskGraphManager): void {
       if (results.length === 0) {
         return { content: [{ type: 'text', text: `No tasks linked to ${targetGraph}::${targetId}` }] };
       }
-      return { content: [{ type: 'text', text: JSON.stringify(results, null, 2) }] };
+      const clean = (_k: string, v: any) => (Array.isArray(v) && v.length === 0 ? undefined : v);
+      return { content: [{ type: 'text', text: JSON.stringify(results, clean, 2) }] };
     },
   );
 }

src/api/tools/tasks/move-task.ts

@@ -26,11 +26,12 @@ export function register(server: McpServer, mgr: TaskGraphManager): void {
           return { content: [{ type: 'text', text: 'Task not found' }], isError: true };
         }
         const task = mgr.getTask(taskId)!;
+        const clean = (_k: string, v: any) => (v === null ? undefined : v);
         return { content: [{ type: 'text', text: JSON.stringify({
           taskId: task.id,
           status: task.status,
           completedAt: task.completedAt,
-        }, null, 2) }] };
+        }, clean, 2) }] };
       } catch (err) {
         if (err instanceof VersionConflictError) {
           return { content: [{ type: 'text', text: JSON.stringify({ error: 'version_conflict', current: err.current, expected: err.expected }) }], isError: true };