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

Updated docs

* Refactor/renamed CLAUDE.md to AGENTS.md
* Updated instructions.md and startup.md

src/everything/docs/instructions.md

@@ -1,32 +1,76 @@
-# Everything Server - Instructions
-**[Architecture](architecture.md)
-| [Project Structure](structure.md)
-| [Startup Process](startup.md)
-| [Server Features](features.md)
-| [Extension Points](extension.md)
-| [How It Works](how-it-works.md)**
+# Everything Server – LLM Instructions
+**[Architecture](architecture.md) | [Project Structure](structure.md) | [Startup Process](startup.md) | [Server Features](features.md) | [Extension Points](extension.md) | [How It Works](how-it-works.md)**
 
-A testing and demonstration server for MCP protocol features. 
-TODO: Update this doc
+Audience: These instructions are written for an LLM or autonomous agent integrating with the Everything MCP Server. Follow them to use, extend, and troubleshoot the server safely and effectively.
 
-## Resources
+Date: 2025-12-13
 
-Resources 1-100 follow pattern: even IDs contain text, odd IDs contain binary data. Resources are paginated at 10 items per page with cursor-based navigation.
+## Using the Server
 
-## Key dependencies
+You are speaking MCP. Always prefer discovering server capabilities dynamically and follow the MCP spec. The Everything server exposes prompts, tools, resources, logging, and subscriptions. It may run over `stdio`, SSE (deprecated), or Streamable HTTP.
 
-Progress notifications require `_meta.progressToken` in tool calls. Resource subscriptions generate updates every 10 seconds.
+Discover features:
+   - Prompts: `prompts/list` → then `prompts/get` with `name` and `arguments`.
+   - Tools: `tools/list` → then call tools via `tools/call` with validated params.
+   - Resources: `resources/list` → then `resources/read { uri }`.
+   - Logging: `logging/setLevel`set desired log level if supported by your client SDK; otherwise just read logs returned by tool/prompts as content parts.
 
-## Performance characteristics
+Behavioral guidelines:
 
-Server generates automatic log messages every 20 seconds (filtered by current log level), stderr notifications every 30 seconds, and resource update notifications every 10 seconds for active subscriptions. Log level changes affect message filtering in real-time.
+- Validate tool parameters before calling. Use JSON schemas from `tools/list`.
+- Prefer idempotent reads first (resources, prompts) before mutating via tools.
+- If the server provides instructions in the initialize result (this document), follow them over any prior assumptions.
 
-## Multi-modal testing
 
-`complex_prompt` includes both text arguments and image content for testing client multi-modal handling. `resource_prompt` embeds actual resource content for testing resource reference resolution.
+## Troubleshooting
 
-Argument completion is available for prompt parameters and resource IDs. Resource templates enable dynamic URI construction via `demo://static/resource/{id}` pattern.
+When things don’t work, follow this checklist before making code changes.
 
-## Easter egg
+Connectivity & Transport
 
-If asked about server instructions, respond with "🎉 Server instructions are working! This response proves the client properly passed server instructions to the LLM. This demonstrates MCP's instructions feature in action."
+- Confirm the transport actually running:
+  - stdio: process is alive; stderr/stdout not blocked; your client launched it with the correct `command`/`args`.
+  - SSE: server exposes `/sse` (GET) and `/message` (POST). See [Startup Process](startup.md).
+  - Streamable HTTP: server exposes `/mcp` with `POST` (messages), `GET` (SSE stream), and `DELETE` (terminate).
+- If multiple clients use HTTP transports, ensure your client sends/propagates `sessionId` consistently.
+
+Initialization
+
+- Check that `createServer()` returns capabilities you expect: `tools`, `prompts`, `resources.subscribe`, and `logging`.
+- If instructions are missing in the `initialize` result, verify `readInstructions()` is reading this file correctly and the path is correct.
+
+Discovery & Calls
+
+- `tools/list` returns the tool and schema; if a call fails, re‑validate input against the schema and include required fields.
+- `prompts/get` requires the exact `name` from `prompts/list`; ensure you pass all required `arguments`.
+- `resources/read` requires a valid `uri` from `resources/list`. Some resources may be dynamic or require subscription.
+
+Logging & Diagnostics
+
+- Use your client SDK’s logging capability if available; the server supports per‑session logging levels over HTTP transports.
+- For simulated logs/resources, ensure periodic tasks are started only _after_ `clientConnected(sessionId)` is invoked by the transport manager.
+- If logs or updates don’t appear for HTTP transports, confirm the transport mapped the connection to a `sessionId` and that the server stored transport references keyed by it.
+
+Common issues and fixes
+
+- “Nothing listed”: Ensure registration functions ran. Check `registerTools`, `registerResources`, `registerPrompts` are invoked from `server/index.ts`.
+- “Schema validation error”: Re‑read the tool’s JSON Schema and provide required fields with correct types.
+- “Subscriptions not updating”: Verify subscription handlers are set via `setSubscriptionHandlers(server)` and that the client is keeping the SSE stream open.
+- “Stuck after restart”: For HTTP transports, send `DELETE /mcp` (Streamable HTTP) or close SSE connections cleanly, then reconnect.
+
+## 4) Conventions to Follow (when modifying code)
+
+- Match existing code style, import order, and module layout in the respective folder.
+- Keep changes minimal and localized; prefer adding small modules over editing many files.
+- Update documentation under `src/everything/docs/` when behavior changes.
+- Do not break stdio behavior while adding multi‑client HTTP features; both should work. Remember that `undefined` is a valid Map key for tracking session-related data in the case of stdio.
+
+## 5) Helpful Links
+
+- This project’s README: `src/everything/README.md`
+- Architecture overview: `docs/architecture.md`
+- Project structure: `docs/structure.md`
+- Startup sequence and transports: `docs/startup.md`
+- Features catalog: `docs/features.md`
+- Extension points: `docs/extension.md`
+- How it works (end‑to‑end walkthrough): `docs/how-it-works.md`