Add skip option for agent setup

README.md

@@ -162,7 +162,8 @@ ktx sl query --connection-id warehouse --measure orders.revenue --format sql
 
 During setup, choose **Ask data questions with ktx MCP** for agent clients.
 Choose **Ask data questions + manage ktx with CLI commands** when an operator
-agent also needs pinned `ktx` admin commands.
+agent also needs pinned `ktx` admin commands. Choose **Skip agent setup for
+now** to leave agent integration incomplete and run `ktx setup --agents` later.
 
 After setup, **ktx** prints **Required before using agents** with the exact
 commands to run. If the output includes `ktx mcp start --project-dir ...`, run

docs-site/content/docs/integrations/agent-clients.mdx

@@ -9,7 +9,9 @@ admin surface for setup, ingest, status, daemon lifecycle, and debugging.
 Run `ktx setup` and select your agent client targets, or configure manually
 using the snippets below. Choose **Ask data questions with ktx MCP** for agent
 clients. Choose **Ask data questions + manage ktx with CLI commands** only when
-a developer or operator agent also needs pinned `ktx` admin commands.
+a developer or operator agent also needs pinned `ktx` admin commands. Choose
+**Skip agent setup for now** to leave agent integration incomplete and run
+`ktx setup --agents` later.
 
 ## Install with setup
 
@@ -43,14 +45,19 @@ ktx setup --agents --target codex --global
 manifest lets status checks report agent readiness and lets future cleanup
 remove only files **ktx** installed.
 
-The interactive command asks two questions:
+The interactive command asks what agents can do first:
 
 ```txt
 ◆  What should agents be allowed to do with this ktx project?
 │  ○ Ask data questions with ktx MCP
 │  ○ Ask data questions + manage ktx with CLI commands
+│  ○ Skip agent setup for now
 └
+```
 
+If you choose an install mode, it then asks which targets to install:
+
+```txt
 ◆  Which agent targets should ktx install?
 │  ◻ Claude Code
 │  ◻ Claude Desktop

packages/cli/src/setup-agents.test.ts

@@ -418,6 +418,11 @@ describe('setup agents', () => {
           label: 'Ask data questions + manage KTX with CLI commands',
           hint: 'Adds an admin CLI skill so agents can run ktx status, sl, wiki, and setup commands.',
         },
+        {
+          value: 'skip',
+          label: 'Skip agent setup for now',
+          hint: 'Leaves agent integration incomplete. You can run ktx setup --agents later.',
+        },
       ],
     });
     expect(prompts.multiselect).toHaveBeenCalledWith(
@@ -427,6 +432,58 @@ describe('setup agents', () => {
     );
   });
 
+  it('lets interactive setup skip agent integration from the connection mode prompt', async () => {
+    const io = makeIo();
+    const prompts = {
+      select: vi.fn(async () => 'skip'),
+      multiselect: vi.fn(async () => {
+        throw new Error('target selection should not run');
+      }),
+      cancel: vi.fn(),
+    };
+
+    await expect(
+      runKtxSetupAgentsStep(
+        {
+          projectDir: tempDir,
+          inputMode: 'auto',
+          yes: false,
+          agents: true,
+          scope: 'project',
+          mode: 'mcp',
+          skipAgents: false,
+        },
+        io.io,
+        { prompts },
+      ),
+    ).resolves.toMatchObject({ status: 'skipped', projectDir: tempDir });
+
+    expect(prompts.select).toHaveBeenCalledWith({
+      message: 'What should agents be allowed to do with this KTX project?',
+      options: [
+        {
+          value: 'mcp',
+          label: 'Ask data questions with KTX MCP',
+          hint: 'Installs the MCP connection and analytics workflow skill. Best for normal use.',
+        },
+        {
+          value: 'mcp-cli',
+          label: 'Ask data questions + manage KTX with CLI commands',
+          hint: 'Adds an admin CLI skill so agents can run ktx status, sl, wiki, and setup commands.',
+        },
+        {
+          value: 'skip',
+          label: 'Skip agent setup for now',
+          hint: 'Leaves agent integration incomplete. You can run ktx setup --agents later.',
+        },
+      ],
+    });
+    expect(prompts.multiselect).not.toHaveBeenCalled();
+    expect(io.stdout()).toContain('Agent integration skipped.');
+    await expect(stat(join(tempDir, '.ktx/agents/install-manifest.json'))).rejects.toThrow();
+    expect(await readKtxSetupState(tempDir)).toEqual({ completed_steps: [] });
+  });
+
   it('prompts for global scope when every selected target supports it', async () => {
     const home = await mkdtemp(join(tmpdir(), 'ktx-setup-agents-home-'));
     const previousHome = process.env.HOME;

packages/cli/src/setup-agents.ts

@@ -21,6 +21,7 @@ export type KtxAgentTarget = 'claude-code' | 'claude-desktop' | 'codex' | 'curso
 export type KtxAgentScope = 'project' | 'global' | 'local';
 /** @internal */
 export type KtxAgentInstallMode = 'mcp' | 'mcp-cli';
+type KtxAgentModePromptChoice = KtxAgentInstallMode | 'skip' | 'back';
 
 export interface KtxSetupAgentsArgs {
   projectDir: string;
@@ -1122,9 +1123,18 @@ export async function runKtxSetupAgentsStep(
               label: 'Ask data questions + manage KTX with CLI commands',
               hint: 'Adds an admin CLI skill so agents can run ktx status, sl, wiki, and setup commands.',
             },
+            {
+              value: 'skip',
+              label: 'Skip agent setup for now',
+              hint: 'Leaves agent integration incomplete. You can run ktx setup --agents later.',
+            },
           ],
-        })) as KtxAgentInstallMode | 'back');
+        })) as KtxAgentModePromptChoice);
   if (mode === 'back') return { status: 'skipped', projectDir: args.projectDir };
+  if (mode === 'skip') {
+    io.stdout.write('│  Agent integration skipped.\n');
+    return { status: 'skipped', projectDir: args.projectDir };
+  }
 
   const targets =
     args.target !== undefined