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

* Updated architecture.md

* Refactor / renamed all addXPrompt, addXTool, and addXResource functions to registerX...

* Added the add tool

src/everything/resources/dynamic.ts

@@ -18,7 +18,7 @@ import {
  *
  * @param server
  */
-export const addDynamicResources = (server: McpServer) => {
+export const registerDynamicResources = (server: McpServer) => {
   const uriBase: string = "test://dynamic/resource";
   const textUriBase: string = `${uriBase}/text`;
   const blobUriBase: string = `${uriBase}/blob`;