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

Adding the get-resource-reference and get-resource-reference tools

* Updated architecture.md

* Added get-resource-links.ts
  - Registers the 'get-resource-reference' tool with the provided McpServer instance.
  - The registered tool retrieves a specified number of resource links and their metadata.

* In get-resource-reference.ts
  - fixed tool description

* In tools/index.ts
  - import registerGetResourceLinksTool
  - in registerTool
    - call registerGetResourceLinksTool

src/everything/tools/get-resource-reference.ts

@@ -26,7 +26,7 @@ const GetResourceReferenceSchema = z.object({
 const name = "get-resource-reference";
 const config = {
   title: "Get Resource Reference Tool",
-  description: "Adds two numbers",
+  description: "Returns a resource reference that can be used by MCP clients",
   inputSchema: GetResourceReferenceSchema,
 };