* In how-it-works.md,
- added a section on conditional tool registration
* In server/index.ts
- import registerConditionalTools
- in an oninitialized handler for the server, call registerConditionalTools
- removed clientConnected from ServerFactoryResponse and all mentions in docs
* In tools/index.ts
- export a registerConditionalTools function
- refactor/move calls to registerGetRootsListTool, registerTriggerElicitationRequestTool, and registerTriggerSamplingRequestTool out of registerTools and into registerConditionalTools
* In server/roots.ts
- only act if client supports roots
- remove setInterval from call to requestRoots. It isn't happening during the initialze handshake anymore, so it doesn't interfere with that process if called immediaately
* In get-roots-list.ts, trigger-elicitation-request.ts, and trigger-sampling-request.ts,
- only register tool if client supports capability
* Throughout the rest of the files, removing all references to `clientConnected`
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
