[WIP] Refactor everything server to be more modular and use recommended APIs.

Adding the annotated message tool

* Updated architecture.md

* Added annotated-message.ts
  - registers a tool that returns a message with annotations on different content types

* In package.json
  - updated TS SDK version

package-lock.json

@@ -3750,7 +3750,7 @@
       "version": "2.0.0",
       "license": "MIT",
       "dependencies": {
-        "@modelcontextprotocol/sdk": "^1.24.0",
+        "@modelcontextprotocol/sdk": "^1.24.3",
         "cors": "^2.8.5",
         "express": "^5.2.1",
         "jszip": "^3.10.1",
@@ -3768,6 +3768,43 @@
         "typescript": "^5.6.2"
       }
     },
+    "src/everything/node_modules/@modelcontextprotocol/sdk": {
+      "version": "1.24.3",
+      "resolved": "https://registry.npmjs.org/@modelcontextprotocol/sdk/-/sdk-1.24.3.tgz",
+      "integrity": "sha512-YgSHW29fuzKKAHTGe9zjNoo+yF8KaQPzDC2W9Pv41E7/57IfY+AMGJ/aDFlgTLcVVELoggKE4syABCE75u3NCw==",
+      "license": "MIT",
+      "dependencies": {
+        "ajv": "^8.17.1",
+        "ajv-formats": "^3.0.1",
+        "content-type": "^1.0.5",
+        "cors": "^2.8.5",
+        "cross-spawn": "^7.0.5",
+        "eventsource": "^3.0.2",
+        "eventsource-parser": "^3.0.0",
+        "express": "^5.0.1",
+        "express-rate-limit": "^7.5.0",
+        "jose": "^6.1.1",
+        "pkce-challenge": "^5.0.0",
+        "raw-body": "^3.0.0",
+        "zod": "^3.25 || ^4.0",
+        "zod-to-json-schema": "^3.25.0"
+      },
+      "engines": {
+        "node": ">=18"
+      },
+      "peerDependencies": {
+        "@cfworker/json-schema": "^4.1.1",
+        "zod": "^3.25 || ^4.0"
+      },
+      "peerDependenciesMeta": {
+        "@cfworker/json-schema": {
+          "optional": true
+        },
+        "zod": {
+          "optional": false
+        }
+      }
+    },
     "src/filesystem": {
       "name": "@modelcontextprotocol/server-filesystem",
       "version": "0.6.3",