test(init): restructure built-in skills describes and cover --built-in + template

Addresses review feedback on PR #60:

- Move the 'built-in skills prompt (interactive init without template)'
  and 'built-in skills in non-interactive environments (CI)' describe
  blocks out of 'init command template mode' and make them siblings
  under a single outer 'init command' describe. The previous nesting
  implied these scenarios ran under template mode when they test the
  opposite, which is misleading when a single describe is selected
  by name.

- Add two test cases in the 'template mode' describe that pin down
  the silent-ignore behavior of --built-in when a template is in play:
  once with skills declared (template skills install, no built-in
  path), once without (no install at all). This closes a previously
  untested invariant that future refactors could otherwise break.

No production code changes. 14 init tests across 3 sibling describes.

Author: nnhhoang

packages/cli/src/__tests__/commands/init.test.ts

@@ -88,7 +88,7 @@ jest.mock('../../util/terminal', () => ({
 
 import { initCommand } from '../../commands/init';
 
-describe('init command template mode', () => {
+describe('init command', () => {
   beforeEach(() => {
     jest.clearAllMocks();
     process.exitCode = undefined;
@@ -121,7 +121,8 @@ describe('init command template mode', () => {
     process.exitCode = undefined;
   });
 
-  it('uses template values and installs multiple skills from same registry without prompts', async () => {
+  describe('template mode', () => {
+    it('uses template values and installs multiple skills from same registry without prompts', async () => {
     mockLoadInitTemplate.mockResolvedValue({
       environments: ['codex'],
       phases: ['requirements', 'design'],
@@ -192,14 +193,49 @@ describe('init command template mode', () => {
     expect(mockUi.warning).toHaveBeenCalledWith('Initialization cancelled.');
   });
 
-  it('sets non-zero exit code when template loading fails', async () => {
-    mockLoadInitTemplate.mockRejectedValue(new Error('Invalid template at /tmp/init.yaml: bad field'));
+    it('sets non-zero exit code when template loading fails', async () => {
+      mockLoadInitTemplate.mockRejectedValue(new Error('Invalid template at /tmp/init.yaml: bad field'));
 
-    await initCommand({ template: '/tmp/init.yaml' });
+      await initCommand({ template: '/tmp/init.yaml' });
 
-    expect(mockUi.error).toHaveBeenCalledWith('Invalid template at /tmp/init.yaml: bad field');
-    expect(process.exitCode).toBe(1);
-    expect(mockConfigManager.setEnvironments).not.toHaveBeenCalled();
+      expect(mockUi.error).toHaveBeenCalledWith('Invalid template at /tmp/init.yaml: bad field');
+      expect(process.exitCode).toBe(1);
+      expect(mockConfigManager.setEnvironments).not.toHaveBeenCalled();
+    });
+
+    it('silently ignores --built-in when the template declares skills', async () => {
+      mockLoadInitTemplate.mockResolvedValue({
+        environments: ['codex'],
+        phases: ['requirements'],
+        skills: [{ registry: 'codeaholicguy/ai-devkit', skill: 'debug' }]
+      });
+
+      await initCommand({ template: './init.yaml', builtIn: true });
+
+      expect(mockSkillManager.addSkill).toHaveBeenCalledTimes(1);
+      expect(mockSkillManager.addSkill).toHaveBeenCalledWith('codeaholicguy/ai-devkit', 'debug');
+      const builtinPrompts = mockPrompt.mock.calls.filter((call: any[]) => {
+        const questions = call[0];
+        return Array.isArray(questions) && questions.some((q: any) => q?.name === 'installBuiltinSkills');
+      });
+      expect(builtinPrompts).toHaveLength(0);
+    });
+
+    it('silently ignores --built-in when the template has no skills declared', async () => {
+      mockLoadInitTemplate.mockResolvedValue({
+        environments: ['codex'],
+        phases: ['requirements']
+      });
+
+      await initCommand({ template: './init.yaml', builtIn: true });
+
+      expect(mockSkillManager.addSkill).not.toHaveBeenCalled();
+      const builtinPrompts = mockPrompt.mock.calls.filter((call: any[]) => {
+        const questions = call[0];
+        return Array.isArray(questions) && questions.some((q: any) => q?.name === 'installBuiltinSkills');
+      });
+      expect(builtinPrompts).toHaveLength(0);
+    });
   });
 
   describe('built-in skills prompt (interactive init without template)', () => {