feat(claude): register the MCP server in user scope by default

`config claude` wrote a per-directory `.mcp.json`, so you had to re-run it in
every checkout you opened — and in a repo that commits `.mcp.json` (this one
does) it dirtied the working tree. Every other integration is already global:
pi, prime-agent and opencode each have one active project, wired once.

Claude Code's user scope is `mcpServers` in `.claude.json`, which applies in
every directory and window. That is now the default. `--scope project`, or an
explicit `-o/--output`, keeps the old per-directory file for a repo that wants
its own pinned project. `--inspect` stays project-scope — it is a debugging
server you turn on for one checkout.

Details worth knowing:

  - The file path is asymmetric: `$CLAUDE_CONFIG_DIR/.claude.json` when that is
    set, but `$HOME/.claude.json` by default — beside `~/.claude/`, not inside
    it. Verified against a live Claude Code run with an isolated config dir.
  - `.claude.json` also holds onboarding state, caches and a per-project map
    that Claude Code rewrites while running, so this merges into the document
    and writes through a temp file + rename.
  - User scope writes no `.mcpctl-project` marker: it scopes nothing to a
    directory, and a marker beside `.claude.json` would sit in $HOME and scope
    every repo under it.
  - `statusline` now resolves directory-scoped `.mcp.json` first (a repo that
    pinned itself wins), then user scope, then the marker.

Scope selection reads Commander's option source rather than process.argv —
argv is the test runner's command line when the command is driven in-process,
which the suite caught immediately.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BVwuCjuMoA13gmzYEfcrNP

src/cli/tests/commands/claude.test.ts

@@ -1,5 +1,5 @@
 import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest';
-import { writeFileSync, readFileSync, mkdtempSync, rmSync, existsSync } from 'node:fs';
+import { writeFileSync, readFileSync, mkdtempSync, rmSync, existsSync, mkdirSync } from 'node:fs';
 import { join } from 'node:path';
 import { tmpdir } from 'node:os';
 import { createConfigCommand } from '../../src/commands/config.js';
@@ -278,3 +278,85 @@ describe('config impersonate', () => {
     expect(output.join('\n')).toContain('No impersonation session to quit');
   });
 });
+
+describe('config claude — user scope', () => {
+  let output: string[];
+  let tmpDir: string;
+  let claudeDir: string;
+  let prior: string | undefined;
+  const log = (...args: string[]): void => { output.push(args.join(' ')); };
+  const claudeJson = (): string => join(claudeDir, '.claude.json');
+
+  beforeEach(() => {
+    output = [];
+    tmpDir = mkdtempSync(join(tmpdir(), 'mcpctl-claude-user-'));
+    claudeDir = join(tmpDir, 'claude-home');
+    mkdirSync(claudeDir, { recursive: true });
+    prior = process.env['CLAUDE_CONFIG_DIR'];
+    process.env['CLAUDE_CONFIG_DIR'] = claudeDir;
+  });
+  afterEach(() => {
+    rmSync(tmpDir, { recursive: true, force: true });
+    if (prior === undefined) delete process.env['CLAUDE_CONFIG_DIR'];
+    else process.env['CLAUDE_CONFIG_DIR'] = prior;
+  });
+
+  const cmd = () => createConfigCommand({ configDeps: {}, log });
+
+  it('registers in .claude.json by default, not a per-directory .mcp.json', async () => {
+    // The whole point: wire it once, not in every checkout you open.
+    await cmd().parseAsync(['claude', '--project', 'homeautomation', '--skip-skills', '--skip-ui'], { from: 'user' });
+    const parsed = JSON.parse(readFileSync(claudeJson(), 'utf-8'));
+    expect(parsed.mcpServers.mcpctl).toEqual({ command: 'mcpctl', args: ['mcp', '-p', 'homeautomation'] });
+    expect(output.join('\n')).toContain('every directory');
+  });
+
+  it('preserves everything else in .claude.json', async () => {
+    // That file also holds onboarding state, caches and the per-project map.
+    writeFileSync(claudeJson(), JSON.stringify({
+      numStartups: 42,
+      mcpServers: { 'taskmaster-ai': { type: 'stdio', command: 'task-master-ai' } },
+      projects: { '/some/repo': { allowedTools: [] } },
+    }));
+    await cmd().parseAsync(['claude', '--project', 'p', '--skip-skills', '--skip-ui'], { from: 'user' });
+    const parsed = JSON.parse(readFileSync(claudeJson(), 'utf-8'));
+    expect(parsed.numStartups).toBe(42);
+    expect(parsed.projects).toEqual({ '/some/repo': { allowedTools: [] } });
+    expect(parsed.mcpServers['taskmaster-ai']).toBeDefined();
+    expect(parsed.mcpServers.mcpctl.args).toEqual(['mcp', '-p', 'p']);
+  });
+
+  it('switching re-points the one entry', async () => {
+    await cmd().parseAsync(['claude', '--project', 'a', '--skip-skills', '--skip-ui'], { from: 'user' });
+    await cmd().parseAsync(['claude', '--project', 'b', '--skip-skills', '--skip-ui'], { from: 'user' });
+    const parsed = JSON.parse(readFileSync(claudeJson(), 'utf-8'));
+    expect(Object.keys(parsed.mcpServers)).toEqual(['mcpctl']);
+    expect(parsed.mcpServers.mcpctl.args).toEqual(['mcp', '-p', 'b']);
+  });
+
+  it('writes no .mcpctl-project marker — user scope is not directory-specific', async () => {
+    // A marker beside .claude.json would sit in $HOME and scope every repo under it.
+    const cwd = process.cwd();
+    process.chdir(tmpDir);
+    try {
+      await cmd().parseAsync(['claude', '--project', 'p', '--skip-ui'], { from: 'user' });
+      expect(existsSync(join(tmpDir, '.mcpctl-project'))).toBe(false);
+      expect(output.join('\n')).toContain('not directory-specific');
+    } finally { process.chdir(cwd); }
+  });
+
+  it('an explicit --output still means the per-directory file', async () => {
+    const outPath = join(tmpDir, '.mcp.json');
+    await cmd().parseAsync(['claude', '--project', 'p', '-o', outPath, '--skip-skills', '--skip-ui'], { from: 'user' });
+    expect(existsSync(outPath)).toBe(true);
+    expect(existsSync(claudeJson())).toBe(false);
+  });
+
+  it('rejects an unknown scope instead of silently picking one', async () => {
+    const prevExit = process.exitCode;
+    await cmd().parseAsync(['claude', '--project', 'p', '--scope', 'global', '--skip-skills'], { from: 'user' });
+    expect(process.exitCode).toBe(1);
+    process.exitCode = prevExit;
+    expect(output.join('\n')).toContain("unknown --scope 'global'");
+  });
+});