Refactor servers to use registerTool/registerResource/registerPrompt APIs

Updated all TypeScript MCP servers to use the new registration API pattern:
- Replaced setRequestHandler(ListToolsRequestSchema) with registerTool()
- Replaced setRequestHandler(GetPromptRequestSchema) with registerPrompt()
- Replaced setRequestHandler(ReadResourceRequestSchema) with registerResource()

Changes:
- sequentialthinking: Migrated 1 tool to registerTool()
- memory: Migrated 9 tools to registerTool()
- filesystem: Migrated 14 tools to registerTool()
- everything: Migrated 11 tools, 3 prompts, and 100 resources to new APIs

Also updated SDK versions to ^1.20.1 across all servers for consistency.

Note: These APIs are not yet available in the current SDK version. This is
preparatory work for when the SDK is updated to support these methods.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

src/sequentialthinking/package.json

@@ -19,7 +19,7 @@
     "watch": "tsc --watch"
   },
   "dependencies": {
-    "@modelcontextprotocol/sdk": "0.5.0",
+    "@modelcontextprotocol/sdk": "^1.20.1",
     "chalk": "^5.3.0",
     "yargs": "^17.7.2"
   },