diff --git a/src/cli/index.ts b/src/cli/index.ts
index 7f37911..dfbbb22 100644
--- a/src/cli/index.ts
+++ b/src/cli/index.ts
@@ -21,7 +21,10 @@ import {
   DrizzlePlanRepository,
   DrizzleTaskRepository,
   DrizzleMessageRepository,
+  DrizzleAgentRepository,
 } from '../db/index.js';
+import { ClaudeAgentManager } from '../agent/index.js';
+import { SimpleGitWorktreeManager } from '../git/index.js';
 
 /** Environment variable for custom port */
 const CW_PORT_ENV = 'CW_PORT';
@@ -51,6 +54,11 @@ async function startServer(port?: number): Promise<void> {
   const planRepository = new DrizzlePlanRepository(db);
   const taskRepository = new DrizzleTaskRepository(db);
   const messageRepository = new DrizzleMessageRepository(db);
+  const agentRepository = new DrizzleAgentRepository(db);
+
+  // Create agent manager with worktree isolation
+  const worktreeManager = new SimpleGitWorktreeManager(process.cwd(), eventBus);
+  const agentManager = new ClaudeAgentManager(agentRepository, worktreeManager, eventBus);
 
   // Create and start server
   const server = new CoordinationServer(
@@ -59,6 +67,7 @@ async function startServer(port?: number): Promise<void> {
     logManager,
     eventBus,
     {
+      agentManager,
       initiativeRepository,
       phaseRepository,
       planRepository,
diff --git a/src/trpc/router.ts b/src/trpc/router.ts
index 3edf19c..699cfd0 100644
--- a/src/trpc/router.ts
+++ b/src/trpc/router.ts
@@ -408,8 +408,8 @@ export const appRouter = router({
    */
   listAgents: publicProcedure
     .query(async ({ ctx }) => {
-      if (!ctx.agentManager) return [];
-      return ctx.agentManager.list();
+      const agentManager = requireAgentManager(ctx);
+      return agentManager.list();
     }),
 
   /**
@@ -463,9 +463,9 @@ export const appRouter = router({
   getAgentQuestions: publicProcedure
     .input(agentIdentifierSchema)
     .query(async ({ ctx, input }): Promise<PendingQuestions | null> => {
-      if (!ctx.agentManager) return null;
+      const agentManager = requireAgentManager(ctx);
       const agent = await resolveAgent(ctx, input);
-      return ctx.agentManager.getPendingQuestions(agent.id);
+      return agentManager.getPendingQuestions(agent.id);
     }),
 
   /**
@@ -474,8 +474,8 @@ export const appRouter = router({
    */
   listWaitingAgents: publicProcedure
     .query(async ({ ctx }) => {
-      if (!ctx.agentManager) return [];
-      const allAgents = await ctx.agentManager.list();
+      const agentManager = requireAgentManager(ctx);
+      const allAgents = await agentManager.list();
       return allAgents.filter(agent => agent.status === 'waiting_for_input');
     }),