[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/docs/extension.md

@@ -0,0 +1,22 @@
+# Everything Server - Extension Points
+**[Architecture](architecture.md)
+| [Project Structure](structure.md)
+| [Startup Process](startup.md)
+| [Server Features](features.md)
+| Extension Points
+| [How It Works](how-it-works.md)**
+
+## Adding Tools
+
+- Create a new file under `tools/` with your `registerXTool(server)` function that registers the tool via `server.registerTool(...)`.
+- Export and call it from `tools/index.ts` inside `registerTools(server)`.
+
+## Adding Prompts
+
+- Create a new file under `prompts/` with your `registerXPrompt(server)` function that registers the prompt via `server.registerPrompt(...)`.
+- Export and call it from `prompts/index.ts` inside `registerPrompts(server)`.
+
+## Adding Resources
+
+- Create a new file under `resources/` with your `registerXResources(server)` function using `server.registerResource(...)` (optionally with `ResourceTemplate`).
+- Export and call it from `resources/index.ts` inside `registerResources(server)`.