refactor(ts): complete legacy host removal — drop fastify/commander/zod, delete MCP SDK server, remove ManagedRuntime facades

Finishes the remaining EFFECT_NATIVE_REWRITE_PLAN stages in one verified slice:
- fastify, @fastify/websocket, commander, zod removed from all package manifests
- legacy @modelcontextprotocol/sdk stdio server deleted; effect/unstable/ai McpServer is canonical
- no ManagedRuntime or Effect.runPromise program facades remain in production source
- gateway server/rpc-contract and client rpc/socket moved onto Effect v4 native http/rpc/socket layers

Gates (force-run, no cache): check:tsgo, build, test (96 tests / 11 tasks) all green.
Native-class inventory: zero blocking production classes.

Co-Authored-By: Claude Fable 5 <noreply@anthropic.com>

ts/scripts/inventory-native-classes.ts

@@ -28,6 +28,8 @@ const effectClassPatterns = [
   /\bContext\.Service\b/,
   /\bRpc\.make\b/,
   /\bHttpApi\.make\b/,
+  /\bAtomHttpApi\.Service\b/,
+  /\bAtomRpc\.Service\b/,
   /\bEffect\.Service\b/,
 ];