[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/resources/index.ts

@@ -1,6 +1,9 @@
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { registerResourceTemplates } from "./templates.js";
 import { registerFileResources } from "./files.js";
+import { fileURLToPath } from "url";
+import { dirname, join } from "path";
+import { readFileSync } from "fs";
 
 /**
  * Register the resources with the MCP server.
@@ -10,3 +13,24 @@ export const registerResources = (server: McpServer) => {
   registerResourceTemplates(server);
   registerFileResources(server);
 };
+
+/**
+ * Reads the server instructions from the corresponding markdown file.
+ * Attempts to load the content of the file located in the `docs` directory.
+ * If the file cannot be loaded, an error message is returned instead.
+ *
+ * @return {string} The content of the server instructions file, or an error message if reading fails.
+ */
+export function readInstructions(): string {
+  const __filename = fileURLToPath(import.meta.url);
+  const __dirname = dirname(__filename);
+  const filePath = join(__dirname, "..", "docs", "instructions.md");
+  let instructions;
+
+  try {
+    instructions = readFileSync(filePath, "utf-8");
+  } catch (e) {
+    instructions = "Server instructions not loaded: " + e;
+  }
+  return instructions;
+}