feat(cli): add mcpctl config prime-agent — proxy MCP + skills sync for prime-agent

Mirror `mcpctl config claude` for prime-agent (which talks to the same mcpctl
proxy MCP gateway over HTTP instead of stdio):

`mcpctl config prime-agent --project X`:
- registers the proxy MCP gateway in ~/.prime/agent/settings.json as
  mcpServers.X = { type: "http", url: <gateway>/projects/X/mcp }, merging with
  any existing servers (e.g. the bundled `sre` project) and preserving all other
  settings
- writes a .mcpctl-project marker so later syncs resolve the project
- syncs the project's skills into ~/.prime/agent/skills/<name>/ as markdown
  skills (prime-agent auto-discovers them at session start)

New `mcpctl skills sync --agent prime-agent` target re-syncs the tree later.

- src/cli/src/config/prime-agent.ts: settings.json read/merge/write helpers
- src/cli/src/utils/prime-agent-skills.ts: prime-agent sync (reuses
  installSkillAtomic + skills-state; skips Claude-only hooks/postInstall)
- completes config.ts/skills.ts wiring; regenerated shell completions
- tests: commands/prime-agent.test.ts + utils/prime-agent-skills.test.ts

src/cli/tests/commands/prime-agent.test.ts

@@ -0,0 +1,147 @@
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
+import { writeFileSync, readFileSync, mkdtempSync, rmSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { createConfigCommand } from '../../src/commands/config.js';
+import type { ApiClient } from '../../src/api-client.js';
+import { DEFAULT_MCPCTL_GATEWAY_URL } from '../../src/config/prime-agent.js';
+
+function mockClient(): ApiClient {
+  return {
+    get: vi.fn(async () => ({})),
+    post: vi.fn(async () => ({ token: 'impersonated-tok', user: { email: 'other@test.com' } })),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+describe('config prime-agent', () => {
+  let client: ReturnType<typeof mockClient>;
+  let output: string[];
+  let tmpDir: string;
+  const log = (...args: string[]) => output.push(args.join(' '));
+
+  let prevCwd: string;
+
+  beforeEach(() => {
+    client = mockClient();
+    output = [];
+    tmpDir = mkdtempSync(join(tmpdir(), 'mcpctl-config-prime-agent-'));
+    // config prime-agent writes the .mcpctl-project marker into cwd, so run
+    // every test from an isolated temp dir to avoid polluting the repo.
+    prevCwd = process.cwd();
+    process.chdir(tmpDir);
+  });
+
+  afterEach(() => {
+    process.chdir(prevCwd);
+    process.exitCode = 0;
+    rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it('requires --project', async () => {
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--skip-skills'], { from: 'user' });
+    expect(output.join('\n')).toContain('--project is required');
+    expect(process.exitCode).toBe(1);
+  });
+
+  it('writes proxy MCP entry into prime-agent settings.json', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--project', 'homeautomation', '-o', settingsPath, '--skip-skills'], { from: 'user' });
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.mcpServers['homeautomation']).toEqual({
+      type: 'http',
+      url: `${DEFAULT_MCPCTL_GATEWAY_URL}/projects/homeautomation/mcp`,
+    });
+    expect(output.join('\n')).toContain('homeautomation');
+  });
+
+  it('merges with existing servers and preserves other settings', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    writeFileSync(settingsPath, JSON.stringify({
+      defaultProvider: 'itaz',
+      mcpServers: {
+        sre: { type: 'http', url: `${DEFAULT_MCPCTL_GATEWAY_URL}/projects/sre/mcp` },
+      },
+    }));
+
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--project', 'proj-1', '-o', settingsPath, '--skip-skills'], { from: 'user' });
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.defaultProvider).toBe('itaz'); // untouched
+    expect(written.mcpServers['sre']).toBeDefined(); // preserved
+    expect(written.mcpServers['proj-1']).toEqual({
+      type: 'http',
+      url: `${DEFAULT_MCPCTL_GATEWAY_URL}/projects/proj-1/mcp`,
+    });
+  });
+
+  it('writes a project marker for later skills sync', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--project', 'sre', '-o', settingsPath, '--skip-skills'], { from: 'user' });
+
+    const markerPath = join(tmpDir, '.mcpctl-project');
+    expect(readFileSync(markerPath, 'utf-8').trim()).toBe('sre');
+  });
+
+  it('--dry-run prints the change without writing', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--project', 'proj-2', '-o', settingsPath, '--dry-run'], { from: 'user' });
+
+    expect(output.join('\n')).toContain('proj-2');
+    // No file should have been created.
+    expect(exceptionSafeRead(settingsPath)).toBeNull();
+  });
+
+  it('does not call the API when --skip-skills is set', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent', '--project', 'proj-3', '-o', settingsPath, '--skip-skills'], { from: 'user' });
+
+    expect(client.get).not.toHaveBeenCalled();
+  });
+
+  it('backward compat: prime-agent-generate still works', async () => {
+    const settingsPath = join(tmpDir, 'settings.json');
+    const cmd = createConfigCommand(
+      { configDeps: { configDir: tmpDir }, log },
+      { client, credentialsDeps: { configDir: tmpDir }, log },
+    );
+    await cmd.parseAsync(['prime-agent-generate', '--project', 'proj-1', '-o', settingsPath, '--skip-skills'], { from: 'user' });
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.mcpServers['proj-1']).toBeDefined();
+  });
+});
+
+function exceptionSafeRead(path: string): string | null {
+  try {
+    return readFileSync(path, 'utf-8');
+  } catch {
+    return null;
+  }
+}

src/cli/tests/completions.test.ts

@@ -234,7 +234,7 @@ describe('agent + chat completions', () => {
   });
 
   it('bash dispatches `create agent` with the correct flags', () => {
-    const createBlock = bashFile.match(/agent\)[\s\S]*?;;/)?.[0] ?? '';
+    const createBlock = bashFile.match(/^\s*agent\)[\s\S]*?;;/m)?.[0] ?? '';
     expect(createBlock).toContain('--llm');
     expect(createBlock).toContain('--system-prompt');
     expect(createBlock).toContain('--default-temperature');

src/cli/tests/utils/prime-agent-skills.test.ts

@@ -0,0 +1,124 @@
+import { describe, it, expect, beforeEach, afterEach, vi } from 'vitest';
+import { readFileSync, mkdirSync, mkdtempSync, rmSync, existsSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir } from 'node:os';
+import { runPrimeAgentSkillsSync } from '../../src/utils/prime-agent-skills.js';
+import { loadState } from '../../src/utils/skills-state.js';
+import type { ApiClient } from '../../src/api-client.js';
+
+function mockClient(overrides: Record<string, unknown> = {}): ApiClient {
+  return {
+    get: vi.fn(async (url: string) => {
+      if (url.includes('/skills/visible')) {
+        return overrides['visible'] ?? [];
+      }
+      if (url.startsWith('/api/v1/skills/')) {
+        const id = url.split('/').pop() as string;
+        const full = (overrides['full'] as Record<string, unknown>)?.[id];
+        if (!full) throw new Error(`no full skill for ${id}`);
+        return full;
+      }
+      if (url.endsWith('/skills?scope=global')) {
+        return overrides['visible'] ?? [];
+      }
+      throw new Error(`unexpected get: ${url}`);
+    }),
+    post: vi.fn(async () => ({})),
+    put: vi.fn(async () => ({})),
+    delete: vi.fn(async () => {}),
+  } as unknown as ApiClient;
+}
+
+const SKILL_MD = `---
+name: sample-skill
+description: A test skill synced into prime-agent.
+---
+
+# Sample Skill
+
+Body text.
+`;
+
+describe('runPrimeAgentSkillsSync', () => {
+  let tmpDir: string;
+  let installRoot: string;
+  let statePath: string;
+  const log = (..._a: unknown[]) => {};
+  const warn = (..._a: unknown[]) => {};
+
+  function deps(client: ApiClient) {
+    return { client, log, warn };
+  }
+
+  beforeEach(() => {
+    tmpDir = mkdtempSync(join(tmpdir(), 'mcpctl-pa-sync-'));
+    installRoot = join(tmpDir, 'skills');
+    statePath = join(tmpDir, 'skills-state.json');
+  });
+
+  afterEach(() => {
+    rmSync(tmpDir, { recursive: true, force: true });
+  });
+
+  it('installs a new markdown skill into the prime-agent skills root', async () => {
+    const visible = [
+      { id: 'skill-1', name: 'sample-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:h1', metadata: {}, scope: 'project' },
+    ];
+    const full = {
+      'skill-1': { id: 'skill-1', name: 'sample-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:h1', content: SKILL_MD, files: {} },
+    };
+    const client = mockClient({ visible, full });
+
+    const result = await runPrimeAgentSkillsSync(
+      { project: 'proj', installRoot, statePath },
+      deps(client),
+    );
+
+    expect(result.installed).toEqual(['sample-skill']);
+    expect(result.errors).toEqual([]);
+
+    const skillDir = join(installRoot, 'sample-skill');
+    expect(existsSync(skillDir)).toBe(true);
+    expect(readFileSync(join(skillDir, 'SKILL.md'), 'utf-8')).toBe(SKILL_MD);
+
+    // State persisted so a re-sync is a no-op.
+    const state = await loadState(statePath);
+    expect(state.skills['sample-skill'].contentHash).toBe('sha256:h1');
+  });
+
+  it('skips unchanged skills on re-sync', async () => {
+    const visible = [
+      { id: 'skill-1', name: 'sample-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:h1', metadata: {}, scope: 'project' },
+    ];
+    const full = {
+      'skill-1': { id: 'skill-1', name: 'sample-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:h1', content: SKILL_MD, files: {} },
+    };
+    const client = mockClient({ visible, full });
+
+    await runPrimeAgentSkillsSync({ project: 'proj', installRoot, statePath }, deps(client));
+    const result = await runPrimeAgentSkillsSync({ project: 'proj', installRoot, statePath }, deps(client));
+
+    expect(result.skipped).toEqual(['sample-skill']);
+    expect(result.installed).toEqual([]);
+  });
+
+  it('syncs the global set when no project is provided', async () => {
+    const visible = [
+      { id: 'skill-2', name: 'global-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:g1', metadata: {}, scope: 'global' },
+    ];
+    const full = {
+      'skill-2': { id: 'skill-2', name: 'global-skill', description: 'd', semver: '1.0.0', contentHash: 'sha256:g1', content: '# global\n', files: {} },
+    };
+    const client = mockClient({ visible, full });
+
+    // Isolate cwd so no stray .mcpctl-project marker is discovered.
+    const empty = join(tmpDir, 'empty');
+    mkdirSync(empty, { recursive: true });
+
+    const result = await runPrimeAgentSkillsSync({ cwd: empty, installRoot, statePath }, deps(client));
+
+    expect(result.installed).toEqual(['global-skill']);
+    const getCalls = (client.get as ReturnType<typeof vi.fn>).mock.calls.map((c) => String(c[0]));
+    expect(getCalls.some((u) => u.includes('scope=global'))).toBe(true);
+  });
+});