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/packages/workbench/package.json

@@ -10,21 +10,11 @@
     "qa:browser": "playwright test"
   },
   "dependencies": {
-    "@effect/ai-anthropic": "4.0.0-beta.78",
-    "@effect/ai-openai": "4.0.0-beta.78",
-    "@effect/ai-openrouter": "4.0.0-beta.78",
     "@effect/atom-react": "4.0.0-beta.78",
-    "@effect/openapi-generator": "4.0.0-beta.78",
-    "@effect/opentelemetry": "4.0.0-beta.78",
     "@effect/platform-browser": "4.0.0-beta.78",
-    "@effect/platform-bun": "4.0.0-beta.78",
-    "@effect/platform-node": "4.0.0-beta.78",
-    "@effect/platform-node-shared": "4.0.0-beta.78",
-    "@effect/tsgo": "0.14.0",
-    "@effect/vitest": "4.0.0-beta.78",
-    "@tanstack/react-query": "^5.75.0",
     "@trustgraph/client": "workspace:*",
     "clsx": "^2.1.0",
+    "effect": "4.0.0-beta.78",
     "lucide-react": "^0.513.0",
     "react": "^19.1.0",
     "react-dom": "^19.1.0",
@@ -32,8 +22,7 @@
     "react-force-graph-2d": "^1.29.1",
     "react-markdown": "^10.1.0",
     "react-router": "^7.6.0",
-    "tailwind-merge": "^3.3.0",
-    "zustand": "^5.0.0"
+    "tailwind-merge": "^3.3.0"
   },
   "devDependencies": {
     "@effect/vitest": "4.0.0-beta.78",

ts/packages/workbench/src/components/notification-toasts.tsx

@@ -20,12 +20,12 @@ export function NotificationToasts() {
   if (notifications.length === 0) return null;
 
   return (
-    <div className="fixed bottom-4 right-4 z-50 flex flex-col gap-2" aria-live="polite">
+    <div className="pointer-events-none fixed bottom-4 right-4 z-50 flex flex-col gap-2" aria-live="polite">
       {notifications.map((n) => (
         <div
           key={n.id}
           className={cn(
-            "flex items-start gap-2 rounded-lg border px-4 py-3 text-sm shadow-lg",
+            "pointer-events-none flex items-start gap-2 rounded-lg border px-4 py-3 text-sm shadow-lg",
             typeStyles[n.type],
           )}
         >
@@ -37,7 +37,7 @@ export function NotificationToasts() {
           </div>
           <button
             onClick={() => removeNotification(n.id)}
-            className="shrink-0 opacity-60 hover:opacity-100"
+            className="pointer-events-auto shrink-0 opacity-60 hover:opacity-100"
             aria-label="Dismiss notification"
           >
             <X className="h-3.5 w-3.5" />

ts/packages/workbench/src/pages/settings.tsx

@@ -266,8 +266,10 @@ export default function SettingsPage() {
             </button>
             <button
               onClick={() => {
-                if (collectionForm.id.trim().length === 0) return;
+                const collectionId = collectionForm.id.trim();
+                if (collectionId.length === 0) return;
                 createCollection(collectionForm);
+                setField({ key: "collection", value: collectionId });
                 setCollectionForm({ id: "", name: "", description: "", tags: "", submitting: false });
                 setCreateOpen(false);
               }}

ts/packages/workbench/src/qa/initial-values.ts

@@ -8,6 +8,7 @@ import {
   type Settings,
   type WorkbenchApiFactory,
 } from "@/atoms/workbench";
+import type { BaseApi } from "@trustgraph/client";
 import { makeMockBaseApi, qaSettingsFromFixture, type MockWorkbenchFixture } from "@/qa/mock-api";
 
 export interface WorkbenchQaWindowConfig {
@@ -19,6 +20,7 @@ export interface WorkbenchQaWindowConfig {
 declare global {
   interface Window {
     __TRUSTGRAPH_WORKBENCH_QA__?: WorkbenchQaWindowConfig;
+    __TRUSTGRAPH_WORKBENCH_QA_API__?: BaseApi;
   }
 }
 
@@ -43,6 +45,7 @@ export function getWorkbenchQaInitialValues(): Iterable<readonly [Atom.Atom<unkn
   const apiFactory: WorkbenchApiFactory = {
     create: () => api,
   };
+  window.__TRUSTGRAPH_WORKBENCH_QA_API__ = api;
   return [
     [apiFactoryAtom as Atom.Atom<unknown>, apiFactory],
     [settingsAtom as Atom.Atom<unknown>, qaSettings(fixture)],

ts/packages/workbench/vite.config.ts

@@ -25,19 +25,21 @@ export default defineConfig({
       "@": path.resolve(__dirname, "./src"),
     },
   },
-  server: {
-    proxy: {
-      "/api/v1/rpc": {
-        target: "ws://localhost:8088/",
-        ws: true,
+  server: isWorkbenchQa
+    ? {}
+    : {
+        proxy: {
+          "/api/v1/rpc": {
+            target: "ws://localhost:8088/",
+            ws: true,
+          },
+          "/api/v1": {
+            target: "http://localhost:8088/",
+          },
+          "/otel": {
+            target: "http://localhost:4328/",
+            rewrite: (p) => p.replace(/^\/otel/, ""),
+          },
+        },
       },
-      "/api/v1": {
-        target: "http://localhost:8088/",
-      },
-      "/otel": {
-        target: "http://localhost:4328/",
-        rewrite: (p) => p.replace(/^\/otel/, ""),
-      },
-    },
-  },
 });