refactor(server): integrate session MCP command stack

packages/server/src/server/agent/agent-manager.test.ts

@@ -1638,6 +1638,40 @@ test("setTitle bumps updatedAt and persists title in the same snapshot write", a
   expect(live!.updatedAt.getTime()).toBeGreaterThan(Date.parse(before!.updatedAt));
 });
 
+test("updateAgentMetadata bumps updatedAt for stored agents", async () => {
+  const workdir = mkdtempSync(join(tmpdir(), "agent-manager-stored-metadata-updated-at-"));
+  const storagePath = join(workdir, "agents");
+  const storage = new AgentStorage(storagePath, logger);
+  const manager = new AgentManager({
+    clients: {
+      codex: new TestAgentClient(),
+    },
+    registry: storage,
+    logger,
+    idFactory: () => "00000000-0000-4000-8000-000000000128",
+  });
+
+  const snapshot = await manager.createAgent({
+    provider: "codex",
+    cwd: workdir,
+  });
+  await manager.closeAgent(snapshot.id);
+
+  const before = await storage.get(snapshot.id);
+  expect(before).not.toBeNull();
+  expect(manager.getAgent(snapshot.id)).toBeNull();
+
+  await manager.updateAgentMetadata(snapshot.id, {
+    title: "Stored title",
+    labels: { role: "worker" },
+  });
+
+  const after = await storage.get(snapshot.id);
+  expect(after?.title).toBe("Stored title");
+  expect(after?.labels).toEqual({ role: "worker" });
+  expect(Date.parse(after!.updatedAt)).toBeGreaterThan(Date.parse(before!.updatedAt));
+});
+
 test("setGeneratedTitle persists generated title when no title exists", async () => {
   const workdir = mkdtempSync(join(tmpdir(), "agent-manager-generated-title-empty-"));
   const storagePath = join(workdir, "agents");

packages/server/src/server/agent/agent-manager.ts

@@ -539,6 +539,13 @@ export class AgentManager {
     return next;
   }
 
+  private nextStoredUpdatedAt(record: StoredAgentRecord): string {
+    const previousMs = Date.parse(record.updatedAt);
+    const nowMs = Date.now();
+    const nextMs = nowMs > previousMs ? nowMs : previousMs + 1;
+    return new Date(nextMs).toISOString();
+  }
+
   hasInFlightRun(agentId: string): boolean {
     const agent = this.agents.get(agentId);
     if (!agent) {
@@ -1360,6 +1367,7 @@ export class AgentManager {
       ...existing,
       ...(updates.title ? { title: updates.title } : {}),
       ...(updates.labels ? { labels: { ...existing.labels, ...updates.labels } } : {}),
+      updatedAt: this.nextStoredUpdatedAt(existing),
     });
   }
 

packages/server/src/server/agent/agent-prompt.ts

@@ -5,13 +5,18 @@ import type { AgentManager, ManagedAgent } from "./agent-manager.js";
 import type { AgentStorage } from "./agent-storage.js";
 import { ensureAgentLoaded } from "./agent-loading.js";
 
+export type AgentRunController = Pick<
+  AgentManager,
+  "getAgent" | "tryRunOutOfBand" | "hasInFlightRun" | "replaceAgentRun" | "streamAgent"
+>;
+
 export interface StartAgentRunOptions {
   replaceRunning?: boolean;
   runOptions?: AgentRunOptions;
 }
 
 export function startAgentRun(
-  agentManager: AgentManager,
+  agentManager: AgentRunController,
   agentId: string,
   prompt: AgentPromptInput,
   logger: Logger,