fix(agent): add model request timeouts and empty-response fallback

docs/plans/state.json

@@ -1,6 +1,6 @@
 {
   "version": "1.0",
-  "updated_at": "2026-02-17",
+  "updated_at": "2026-02-18",
   "description": "Tracks the status of all Flynn plans and implementation phases",
   "plans": {
     "makefile-skills-convenience-targets": {
@@ -5076,10 +5076,22 @@
         "docs/plans/state.json"
       ],
       "test_status": "pnpm test:run src/session/manager.test.ts src/gateway/handlers/handlers.test.ts + pnpm typecheck passing"
+    },
+    "native-agent-model-timeout-hardening": {
+      "status": "completed",
+      "date": "2026-02-18",
+      "updated": "2026-02-18",
+      "summary": "Added hard per-request model timeouts in `NativeAgent` (`modelTimeoutMs`, default 120000ms) to fail fast when providers hang, covering both single-turn and tool-loop model calls. Also added empty-final-response normalization to avoid silent blank replies and added regression tests for timeout and empty-response cases.",
+      "files_modified": [
+        "src/backends/native/agent.ts",
+        "src/backends/native/agent.test.ts",
+        "docs/plans/state.json"
+      ],
+      "test_status": "pnpm test:run src/backends/native/agent.test.ts passing"
     }
   },
   "overall_progress": {
-    "total_test_count": 1887,
+    "total_test_count": 1889,
     "all_tests_passing": true,
     "p0_completion": "3/3 (100%)",
     "p1_completion": "4/4 (100%)",

src/backends/native/agent.test.ts

@@ -110,6 +110,43 @@ describe('NativeAgent', () => {
     const history = agent.getHistory();
     expect(history[history.length - 1]).toEqual({ role: 'assistant', content: 'Operation cancelled by user.' });
   });
+
+  it('returns fallback text when model response is empty', async () => {
+    const mockClient: ModelClient = {
+      chat: vi.fn().mockResolvedValue({
+        content: '',
+        stopReason: 'end_turn',
+        usage: { inputTokens: 10, outputTokens: 5 },
+      }),
+    };
+
+    const agent = new NativeAgent({
+      modelClient: mockClient,
+      systemPrompt: 'You are helpful.',
+    });
+
+    const response = await agent.process('Hi');
+    expect(response).toBe('I could not generate a response for that. Please try again.');
+    const history = agent.getHistory();
+    expect(history[history.length - 1]).toEqual({
+      role: 'assistant',
+      content: 'I could not generate a response for that. Please try again.',
+    });
+  });
+
+  it('times out single-turn model calls', async () => {
+    const mockClient: ModelClient = {
+      chat: vi.fn().mockImplementation(() => new Promise<ChatResponse>(() => {})),
+    };
+
+    const agent = new NativeAgent({
+      modelClient: mockClient,
+      systemPrompt: 'You are helpful.',
+      modelTimeoutMs: 10,
+    });
+
+    await expect(agent.process('Hi')).rejects.toThrow('Model request timed out after 10ms');
+  });
 });
 
 // Simple test tool
@@ -611,4 +648,65 @@ describe('NativeAgent tool loop', () => {
     expect(response).toBe('Got both results');
     expect(mockClient.chat).toHaveBeenCalledTimes(2);
   });
+
+  it('returns fallback text when tool loop final response is empty', async () => {
+    const mockClient: ModelClient = {
+      chat: vi
+        .fn()
+        .mockResolvedValueOnce({
+          content: '',
+          stopReason: 'tool_use',
+          usage: { inputTokens: 10, outputTokens: 5 },
+          toolCalls: [{ id: 'call_1', name: 'test.echo', args: { text: 'hello' } }],
+        })
+        .mockResolvedValueOnce({
+          content: '',
+          stopReason: 'end_turn',
+          usage: { inputTokens: 12, outputTokens: 4 },
+        }),
+    };
+
+    const registry = new ToolRegistry();
+    registry.register(echoTool);
+    const hooks = new HookEngine({ confirm: [], log: [], silent: [] });
+    const executor = new ToolExecutor(registry, hooks);
+
+    const agent = new NativeAgent({
+      modelClient: mockClient,
+      systemPrompt: 'You are helpful.',
+      toolRegistry: registry,
+      toolExecutor: executor,
+    });
+
+    const response = await agent.process('echo hello');
+    expect(response).toBe('I could not generate a response for that. Please try again.');
+    const history = agent.getHistory();
+    expect(history[history.length - 1]).toEqual({
+      role: 'assistant',
+      content: 'I could not generate a response for that. Please try again.',
+    });
+  });
+
+  it('times out tool-loop model calls and returns an error message', async () => {
+    const mockClient: ModelClient = {
+      chat: vi.fn().mockImplementation(() => new Promise<ChatResponse>(() => {})),
+    };
+
+    const registry = new ToolRegistry();
+    registry.register(echoTool);
+    const hooks = new HookEngine({ confirm: [], log: [], silent: [] });
+    const executor = new ToolExecutor(registry, hooks);
+
+    const agent = new NativeAgent({
+      modelClient: mockClient,
+      systemPrompt: 'You are helpful.',
+      toolRegistry: registry,
+      toolExecutor: executor,
+      modelTimeoutMs: 10,
+    });
+
+    const response = await agent.process('echo hello');
+    expect(response).toContain('Error in tool loop');
+    expect(response).toContain('Model request timed out after 10ms');
+  });
 });

src/backends/native/agent.ts

@@ -40,6 +40,8 @@ export interface NativeAgentConfig {
   toolPolicyContext?: ToolPolicyContext;
   /** Collector for outbound attachments queued by tools (e.g. media.send). */
   attachmentCollector?: OutboundAttachmentCollector;
+  /** Hard timeout for each model request in milliseconds. */
+  modelTimeoutMs?: number;
 }
 
 // Internal message type for the tool loop — supports both text and structured content blocks.
@@ -55,6 +57,9 @@ interface PseudoToolUse {
 }
 
 export class NativeAgent {
+  private static readonly EMPTY_RESPONSE_FALLBACK =
+    'I could not generate a response for that. Please try again.';
+  private static readonly DEFAULT_MODEL_TIMEOUT_MS = 120_000;
   private modelClient: ModelClient | ModelRouter;
   private systemPrompt: string;
   private session?: Session;
@@ -72,6 +77,7 @@ export class NativeAgent {
   private _lastToolFingerprint?: string;
   private _cancelRequested = false;
   private _runInProgress = false;
+  private modelTimeoutMs: number;
 
   constructor(config: NativeAgentConfig) {
     this.modelClient = config.modelClient;
@@ -83,6 +89,9 @@ export class NativeAgent {
     this.onToolUse = config.onToolUse;
     this._toolPolicyContext = config.toolPolicyContext;
     this._attachmentCollector = config.attachmentCollector;
+    this.modelTimeoutMs = Number.isFinite(config.modelTimeoutMs)
+      ? Math.max(1, Math.floor(config.modelTimeoutMs as number))
+      : NativeAgent.DEFAULT_MODEL_TIMEOUT_MS;
   }
 
   private get history(): Message[] {
@@ -145,13 +154,15 @@ export class NativeAgent {
     this._totalUsage.outputTokens += response.usage.outputTokens;
     this._callCount++;
 
+    const normalizedContent = this.normalizeAssistantContent(response.content);
+
     // Prepend thinking content if present
-    let finalContent = response.content;
+    let finalContent = normalizedContent;
     if (response.thinkingContent) {
-      finalContent = `<thinking>\n${response.thinkingContent}\n</thinking>\n\n${response.content}`;
+      finalContent = `<thinking>\n${response.thinkingContent}\n</thinking>\n\n${normalizedContent}`;
     }
 
-    const assistantMsg: Message = { role: 'assistant', content: response.content };
+    const assistantMsg: Message = { role: 'assistant', content: normalizedContent };
     this.addToHistory(assistantMsg);
 
     return finalContent;
@@ -230,13 +241,14 @@ export class NativeAgent {
           && response.toolCalls && response.toolCalls.length > 0;
         if (!wantsToolUse) {
           const pseudoToolUse = this.extractPseudoToolUse(response.content);
-          let finalContent = pseudoToolUse
+          const baseContent = pseudoToolUse
             ? this.buildPseudoToolUseWarning(response.content, pseudoToolUse)
-            : response.content;
+            : this.normalizeAssistantContent(response.content);
+          let finalContent = baseContent;
           if (response.thinkingContent) {
-            finalContent = `<thinking>\n${response.thinkingContent}\n</thinking>\n\n${finalContent}`;
+            finalContent = `<thinking>\n${response.thinkingContent}\n</thinking>\n\n${baseContent}`;
           }
-          const assistantMsg: Message = { role: 'assistant', content: finalContent };
+          const assistantMsg: Message = { role: 'assistant', content: baseContent };
           this.addToHistory(assistantMsg);
           return finalContent;
         }
@@ -411,10 +423,27 @@ export class NativeAgent {
   }
 
   private async chatWithRouter(request: ChatRequest): Promise<ChatResponse> {
-    if ('getClient' in this.modelClient) {
-      return (this.modelClient as ModelRouter).chat(request, this.currentTier);
+    const requestPromise = 'getClient' in this.modelClient
+      ? (this.modelClient as ModelRouter).chat(request, this.currentTier)
+      : this.modelClient.chat(request);
+
+    let timer: NodeJS.Timeout | undefined;
+    const timeoutPromise = new Promise<never>((_, reject) => {
+      timer = setTimeout(() => {
+        const error = new Error(`Model request timed out after ${this.modelTimeoutMs}ms`);
+        error.name = 'TimeoutError';
+        reject(error);
+      }, this.modelTimeoutMs);
+      timer.unref?.();
+    });
+
+    try {
+      return await Promise.race([requestPromise, timeoutPromise]);
+    } finally {
+      if (timer) {
+        clearTimeout(timer);
+      }
     }
-    return this.modelClient.chat(request);
   }
 
   private addToHistory(msg: Message): void {
@@ -560,4 +589,11 @@ export class NativeAgent {
       rawContent,
     ].join('\n');
   }
+
+  private normalizeAssistantContent(content: string): string {
+    if (content.trim().length > 0) {
+      return content;
+    }
+    return NativeAgent.EMPTY_RESPONSE_FALLBACK;
+  }
 }