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
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