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/useAutoResize.ts

@@ -4,15 +4,17 @@ import { App } from "../app";
 /**
  * React hook that automatically reports UI size changes to the host.
  *
- * Uses ResizeObserver to watch `document.body` and `document.documentElement` for
+ * Uses `ResizeObserver` to watch `document.body` and `document.documentElement` for
  * size changes and sends `ui/notifications/size-changed` notifications.
  *
+ * The hook automatically cleans up the `ResizeObserver` when the component unmounts.
+ *
  * **Note**: This hook is rarely needed since the {@link useApp} hook automatically enables
  * auto-resize by default. This hook is provided for advanced cases where you
  * create the {@link App} manually with `autoResize: false` and want to add auto-resize
  * behavior later.
  *
- * @param app - The connected App instance, or null during initialization
+ * @param app - The connected {@link App} instance, or null during initialization
  * @param elementRef - Currently unused. The hook always observes `document.body`
  *   and `document.documentElement` regardless of this value. Passing a ref will
  *   cause unnecessary effect re-runs; omit this parameter.
@@ -31,7 +33,7 @@ import { App } from "../app";
  *       { autoResize: false } // Disable default auto-resize
  *     );
  *
- *     const transport = new PostMessageTransport(window.parent);
+ *     const transport = new PostMessageTransport(window.parent, window.parent);
  *     myApp.connect(transport)
  *       .then(() => setApp(myApp))
  *       .catch((err) => setError(err));