[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/how-it-works.md

@@ -0,0 +1,34 @@
+# Everything Server - How It Works
+**[Architecture](architecture.md)
+| [Project Structure](structure.md)
+| [Startup Process](startup.md)
+| [Server Features](features.md)
+| [Extension Points](extension.md)
+| How It Works**
+
+## Resource Subscriptions
+
+Each client manages its own resource subscriptions and receives notifications only for the URIs it subscribed to, independent of other clients.
+
+### Module: `resources/subscriptions.ts`
+
+- Tracks subscribers per URI: `Map<uri, Set<sessionId>>`.
+- Installs handlers via `setSubscriptionHandlers(server)` to process subscribe/unsubscribe requests and keep the map updated.
+- Updates are started/stopped on demand by the `toggle-subscriber-updates` tool, which calls `beginSimulatedResourceUpdates(server, sessionId)` and `stopSimulatedResourceUpdates(sessionId)`.
+- `cleanup(sessionId?)` calls `stopSimulatedResourceUpdates(sessionId)` to clear intervals and remove session‑scoped state.
+
+## Session‑scoped Resources
+
+### Module: `resources/session.ts`
+
+- `getSessionResourceURI(name: string)`: Builds a session resource URI: `demo://resource/session/<name>`.
+- `registerSessionResource(server, resource, type, payload)`: Registers a resource with the given `uri`, `name`, and `mimeType`, returning a `resource_link`. The content is served from memory for the life of the session only. Supports `type: "text" | "blob"` and returns data in the corresponding field.
+- Intended usage: tools can create and expose per-session artifacts without persisting them. For example, `tools/gzip-file-as-resource.ts` compresses fetched content, registers it as a session resource with `mimeType: application/gzip`, and returns either a `resource_link` or an inline `resource` based on `outputType`.
+
+## Simulated Logging
+
+### Module: `server/logging.ts`
+
+- Periodically sends randomized log messages at different levels. Messages can include the session ID for clarity during demos.
+- Started/stopped on demand via the `toggle-logging` tool, which calls `beginSimulatedLogging(server, sessionId?)` and `stopSimulatedLogging(sessionId?)`. Note that transport disconnect triggers `cleanup()` which also stops any active intervals.
+- Uses `server.sendLoggingMessage({ level, data }, sessionId?)` so that the client’s configured minimum logging level is respected by the SDK.