Merge branch 'v2/main' into v2/docs/1822-migration-guide

Took v2/main's project-layout line and quality-gate table (adding
verify:dep-lockstep), keeping this branch's migration-guide mention and
prettier table alignment.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HDdo1rNRVQnVRRdsqSrvG3

clients/cli/package.json

@@ -32,10 +32,6 @@
     "format:check": "prettier --check src __tests__ \"*.{ts,tsx,mts,cts,js,jsx,mjs,cjs}\""
   },
   "dependencies": {
-    "@modelcontextprotocol/client": "2.0.0-beta.5",
-    "@modelcontextprotocol/core": "2.0.0-beta.5",
-    "@modelcontextprotocol/server": "2.0.0-beta.5",
-    "@modelcontextprotocol/server-legacy": "2.0.0-beta.5",
     "@napi-rs/keyring": "^1.3.0",
     "ajv": "^8.17.1",
     "atomically": "^2.1.1",
@@ -43,7 +39,7 @@
     "open": "^10.2.0",
     "pino": "^9.14.0",
     "undici": "^8.5.0",
-    "zod": "^4.3.6"
+    "zod": "^4.4.3"
   },
   "devDependencies": {
     "@eslint/js": "^10.0.1",