Improve JSDoc comments with cross-references and clarifications (#254)

Key improvements:
- Add `{@link}` cross-references throughout the codebase to make API
  documentation navigable and help AI models understand relationships
- Use `{@link module!Export}` syntax for cross-module references
- Add backticks for inline code formatting (`ResizeObserver`, `App`, etc)
- Fix `PostMessageTransport` examples to show required two-argument form
- Clarify `onteardown` callback return type requirement
- Document React hooks cleanup behavior and Strict Mode considerations
- Add tool visibility example for `registerAppTool`
- Add CSP example for `registerAppResource`
- Fix notification direction documentation in `spec.types.ts`

TypeDoc config migrated from `typedoc.json` to `typedoc.config.mjs` to:
- Support custom `@description` block tag
- Add `intentionallyNotExported` for internal types
- Include `src/server/index.ts` entry point

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

src/react/useApp.tsx

@@ -5,27 +5,29 @@ import { App, McpUiAppCapabilities, PostMessageTransport } from "../app";
 export * from "../app";
 
 /**
- * Options for configuring the useApp hook.
+ * Options for configuring the {@link useApp} hook.
  *
- * Note: This interface does NOT expose App options like `autoResize`.
- * The hook creates the App with default options (autoResize: true). If you need
- * custom App options, create the App manually instead of using this hook.
+ * Note: This interface does NOT expose {@link App} options like `autoResize`.
+ * The hook creates the `App` with default options (`autoResize: true`). If you
+ * need custom `App` options, create the `App` manually instead of using this hook.
  *
  * @see {@link useApp} for the hook that uses these options
- * @see {@link useAutoResize} for manual auto-resize control with custom App options
+ * @see {@link useAutoResize} for manual auto-resize control with custom `App` options
  */
 export interface UseAppOptions {
   /** App identification (name and version) */
   appInfo: Implementation;
-  /** Features and capabilities this app provides */
+  /**
+   * Declares what features this app supports.
+   */
   capabilities: McpUiAppCapabilities;
   /**
-   * Called after App is created but before connection.
+   * Called after {@link App} is created but before connection.
    *
    * Use this to register request/notification handlers that need to be in place
    * before the initialization handshake completes.
    *
-   * @param app - The newly created App instance
+   * @param app - The newly created `App` instance
    *
    * @example Register a notification handler
    * ```typescript
@@ -45,10 +47,10 @@ export interface UseAppOptions {
 }
 
 /**
- * State returned by the useApp hook.
+ * State returned by the {@link useApp} hook.
  */
 export interface AppState {
-  /** The connected App instance, null during initialization */
+  /** The connected {@link App} instance, null during initialization */
   app: App | null;
   /** Whether initialization completed successfully */
   isConnected: boolean;
@@ -59,16 +61,19 @@ export interface AppState {
 /**
  * React hook to create and connect an MCP App.
  *
- * This hook manages the complete lifecycle of an {@link App}: creation, connection,
- * and cleanup. It automatically creates a {@link PostMessageTransport} to window.parent
- * and handles initialization.
+ * This hook manages {@link App} creation and connection. It automatically
+ * creates a {@link PostMessageTransport} to window.parent and handles
+ * initialization.
+ *
+ * This hook is part of the optional React integration. The core SDK (`App`,
+ * `PostMessageTransport`) is framework-agnostic and can be used with any UI
+ * framework or vanilla JavaScript.
  *
  * **Important**: The hook intentionally does NOT re-run when options change
  * to avoid reconnection loops. Options are only used during the initial mount.
- *
- * **Note**: This is part of the optional React integration. The core SDK
- * (App, PostMessageTransport) is framework-agnostic and can be
- * used with any UI framework or vanilla JavaScript.
+ * Furthermore, the `App` instance is NOT closed on unmount. This avoids cleanup
+ * issues during React Strict Mode's double-mount cycle. If you need to
+ * explicitly close the `App`, call {@link App.close} manually.
  *
  * @param options - Configuration for the app
  * @returns Current connection state and app instance. If connection fails during