feat(cli): add new commands and refactor into cli/ folder

New commands:
- `marionette --version` / `-v` / `version` — print installed version
- `marionette status` — check if the server is running
- `marionette logs` — tail the server log file (cross-platform)
- `marionette update` — check for newer GitHub releases
- `marionette uninstall` — full cleanup with --yes/-y flag to skip prompt
- `marionette --help` / `-h` — improved help with all commands listed

Refactor:
- Split monolithic cli.ts (750+ lines) into cli/ folder with one file per command
- Shared utilities (distDir, execAsync, isPortInUse, getVersion, shellRcPath) extracted to cli/utils.ts
- Unified 6 duplicate platform setup functions (LaunchAgent/systemd/WindowsTask) into 3 parameterized ones
- Parallelised independent operations with Promise.all (port kills, service unloads, MCP+hooks cleanup, auto-start pairs)

Bump version to 1.1.0

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: yarin-mag

.gitignore

@@ -72,3 +72,4 @@ RELEASING.md
 LAUNCH_STRATEGY.md
 messup-fixes.md
 .claude/
+v2_design/

apps/server/package.json

@@ -1,9 +1,10 @@
 {
   "name": "marionette-server",
+  "version": "1.1.0",
   "private": true,
   "type": "module",
   "bin": {
-    "marionette": "./dist/cli.js"
+    "marionette": "./dist/cli/index.js"
   },
   "scripts": {
     "dev": "tsx watch src/index.ts",