feat(pi): add native pi integration — extension, config pi, skills --agent pi

- src/pi-ext/: self-contained pi extension (mcpctl-pi.ts + vendored
  mcp-http client) that talks JSON-RPC directly to mcplocal and registers
  project MCP tools as native pi tools. No MCP client, no ~/.claude.
- Persistent per-project session so gated projects ungate on begin_session.
- /mcpctl command: status, switch project (GUI), refresh tools, sync skills.
- mcpctl config pi: installs extension, wires pi settings, persists active
  project, syncs skills into ~/.pi/agent/skills.
- skills sync: add --agent pi (target install root).
- docs + tests.

src/cli/tests/utils/pi-settings.test.ts

@@ -0,0 +1,92 @@
+import { describe, it, expect, beforeEach, afterEach } from 'vitest';
+import { mkdtempSync, rmSync, mkdirSync, writeFileSync, readFileSync } from 'node:fs';
+import { join } from 'node:path';
+import { tmpdir, homedir } from 'node:os';
+import { agentInstallRoot } from '../../src/commands/skills.js';
+import {
+  registerWithPi,
+  installExtensionFiles,
+} from '../../src/utils/pi-settings.js';
+
+describe('skills agentInstallRoot', () => {
+  it('maps claude (default) to ~/.claude/skills', () => {
+    expect(agentInstallRoot(undefined)).toBe(join(homedir(), '.claude', 'skills'));
+    expect(agentInstallRoot('claude')).toBe(join(homedir(), '.claude', 'skills'));
+  });
+  it('maps pi to ~/.pi/agent/skills', () => {
+    expect(agentInstallRoot('pi')).toBe(join(homedir(), '.pi', 'agent', 'skills'));
+  });
+  it('maps prime-agent to ~/.prime/agent/skills', () => {
+    expect(agentInstallRoot('prime-agent')).toBe(join(homedir(), '.prime', 'agent', 'skills'));
+  });
+});
+
+describe('pi-settings util', () => {
+  let tmp: string;
+
+  beforeEach(() => {
+    tmp = mkdtempSync(join(tmpdir(), 'mcpctl-pi-settings-'));
+  });
+  afterEach(() => {
+    rmSync(tmp, { recursive: true, force: true });
+  });
+
+  it('registers extension + skills dir into an empty settings file', async () => {
+    const settingsPath = join(tmp, 'settings.json');
+    const extPath = join(tmp, 'ext', 'mcpctl-pi.ts');
+    const skillsDir = join(tmp, 'skills');
+
+    const { addedExtensions, addedSkills } = await registerWithPi(settingsPath, extPath, skillsDir);
+
+    expect(addedExtensions).toEqual([extPath]);
+    expect(addedSkills).toEqual([skillsDir]);
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.extensions).toEqual([extPath]);
+    expect(written.skills).toEqual([skillsDir]);
+  });
+
+  it('is idempotent — running twice does not duplicate entries', async () => {
+    const settingsPath = join(tmp, 'settings.json');
+    const extPath = join(tmp, 'ext', 'mcpctl-pi.ts');
+    const skillsDir = join(tmp, 'skills');
+
+    await registerWithPi(settingsPath, extPath, skillsDir);
+    const second = await registerWithPi(settingsPath, extPath, skillsDir);
+
+    expect(second.addedExtensions).toEqual([]);
+    expect(second.addedSkills).toEqual([]);
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.extensions).toEqual([extPath]);
+    expect(written.skills).toEqual([skillsDir]);
+  });
+
+  it('preserves existing settings keys', async () => {
+    const settingsPath = join(tmp, 'settings.json');
+    mkdirSync(tmp, { recursive: true });
+    writeFileSync(settingsPath, JSON.stringify({ theme: 'dark', packages: ['git:foo/bar'] }, null, 2));
+
+    await registerWithPi(settingsPath, '/abs/ext.ts', '/abs/skills');
+
+    const written = JSON.parse(readFileSync(settingsPath, 'utf-8'));
+    expect(written.theme).toBe('dark');
+    expect(written.packages).toEqual(['git:foo/bar']);
+    expect(written.extensions).toEqual(['/abs/ext.ts']);
+    expect(written.skills).toEqual(['/abs/skills']);
+  });
+
+  it('copies the extension files into the pi extension dir', async () => {
+    const srcDir = join(tmp, 'src-pi-ext');
+    const destDir = join(tmp, 'dest-ext');
+    mkdirSync(srcDir, { recursive: true });
+    writeFileSync(join(srcDir, 'mcpctl-pi.ts'), '// extension\n');
+    writeFileSync(join(srcDir, 'mcp-http.ts'), '// client\n');
+
+    const written = await installExtensionFiles(srcDir, destDir);
+
+    expect(written).toHaveLength(2);
+    expect(readFileSync(join(destDir, 'mcpctl-pi.ts'), 'utf-8')).toBe('// extension\n');
+    expect(readFileSync(join(destDir, 'mcp-http.ts'), 'utf-8')).toBe('// client\n');
+  });
+});