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

Finalized Roots list changed handling and initial request. Final fit and finish work.

* Updated architecture.md
  - Added links to other docs
  - Refactor/extracted sections into extension.md, features.md, how-it-works.md, startup.md, and structure.md

* Removed everything.ts
  - all features are ported

* In roots.ts
  - refactor/renaned setRootsListChangedHandler to syncRoots
  - refactor handler logic to requestRoots function
  - Calls for roots list directly to get initial list

* In server/index.ts
  - import setRootsListChangedHandler
  - in clientConnected callback
    - call setRootsListChangedHandler passing server and sessionId

* In sse.ts, stdio.ts, and streamableHttp.ts
  - update inline and function docs

* In index.ts,
  - updated usage output

* In server/index.ts
  - refactor/extracted readInstructions to resources/index.ts
  - defined ServerFactoryResponse response type

src/everything/server/index.ts

@@ -1,19 +1,40 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
-import { dirname, join } from "path";
-import { readFileSync } from "fs";
-import { fileURLToPath } from "url";
 import {
   setSubscriptionHandlers,
   stopSimulatedResourceUpdates,
 } from "../resources/subscriptions.js";
 import { registerTools } from "../tools/index.js";
-import { registerResources } from "../resources/index.js";
+import { registerResources, readInstructions } from "../resources/index.js";
 import { registerPrompts } from "../prompts/index.js";
 import { stopSimulatedLogging } from "./logging.js";
-import { setRootsListChangedHandler } from "./roots.js";
+import { syncRoots } from "./roots.js";
 
-// Everything Server factory
-export const createServer = () => {
+// Server Factory response
+export type ServerFactoryResponse = {
+  server: McpServer;
+  clientConnected: (sessionId?: string) => void;
+  cleanup: (sessionId?: string) => void;
+};
+
+/**
+ * `ServerInstance` factory
+ *
+ * This function initializes a `McpServer` with specific capabilities and instructions,
+ * registers tools, resources, and prompts, and configures resource subscription handlers.
+ *
+ * It returns the server instance along with callbacks for post-connection setup and cleanup tasks.
+ *
+ * @function
+ * @returns {ServerFactoryResponse} An object containing the server instance, a `clientConnected` callback
+ * for managing new client sessions, and a `cleanup` function for handling server-side cleanup when
+ * a session ends.
+ *
+ * Properties of the returned object:
+ * - `server` {Object}: The initialized server instance.
+ * - `clientConnected` {Function}: A post-connect callback to enable operations that require a `sessionId`.
+ * - `cleanup` {Function}: Function to perform cleanup operations for a closing session.
+ */
+export const createServer: () => ServerFactoryResponse = () => {
   // Read the server instructions
   const instructions = readInstructions();
 
@@ -49,32 +70,17 @@ export const createServer = () => {
   // Set resource subscription handlers
   setSubscriptionHandlers(server);
 
-  // Return server instance, client connection handler, and cleanup function
+  // Return the ServerFactoryResponse
   return {
     server,
     clientConnected: (sessionId?: string) => {
-      // Set the roots list changed handler
-      setRootsListChangedHandler(server, sessionId);
+      // Set a roots list changed handler and fetch the initial roots list from the client
+      syncRoots(server, sessionId);
     },
     cleanup: (sessionId?: string) => {
       // Stop any simulated logging or resource updates that may have been initiated.
       stopSimulatedLogging(sessionId);
       stopSimulatedResourceUpdates(sessionId);
     },
-  };
+  } satisfies ServerFactoryResponse;
 };
-
-// Read the server instructions from a file
-function readInstructions(): string {
-  const __filename = fileURLToPath(import.meta.url);
-  const __dirname = dirname(__filename);
-  const filePath = join(__dirname, "..", "docs", "server-instructions.md");
-  let instructions;
-
-  try {
-    instructions = readFileSync(filePath, "utf-8");
-  } catch (e) {
-    instructions = "Server instructions not loaded: " + e;
-  }
-  return instructions;
-}