feat: bump typescript (#14507)

<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit

* **Chores**
  * Upgraded TypeScript toolchain to v5.9.3 across packages and tooling.
* Removed legacy ts-node and migrated developer tooling to newer
runtimes (tsx/SWC) where applicable.
* **Documentation**
* Updated developer CLI docs and runtime behavior notes to reflect the
new loader/runtime for running TypeScript files; no changes to public
APIs or end-user behavior.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->

tools/cli/src/run.ts

@@ -11,11 +11,15 @@ interface RunScriptOptions {
 }
 
 const currentDir = Path.dir(import.meta.url);
+const serverRuntimeLoader = currentDir
+  .join('../register.js')
+  .toFileUrl()
+  .toString();
 
 const ignoreLoaderScripts = [
   'vitest',
   'vite',
-  'ts-node',
+  'tsx',
   'prisma',
   'cap',
   'tsc',
@@ -161,13 +165,15 @@ export class RunCommand extends PackageCommand {
     args = extractedArgs;
 
     const bin = args[0] === 'yarn' ? args[1] : args[0];
-
-    const loader = currentDir.join('../register.js').toFileUrl().toString();
+    const loader = pkg.name === '@affine/server' ? serverRuntimeLoader : 'tsx';
+    const hasKnownLoader =
+      process.env.NODE_OPTIONS?.includes('tsx') ||
+      process.env.NODE_OPTIONS?.includes(serverRuntimeLoader);
 
     // very simple test for auto ts/mjs scripts
     const isLoaderRequired =
       !ignoreLoaderScripts.some(ignore => new RegExp(ignore).test(bin)) ||
-      process.env.NODE_OPTIONS?.includes('ts-node/esm') ||
+      hasKnownLoader ||
       process.env.NODE_OPTIONS?.includes(loader);
 
     let NODE_OPTIONS = process.env.NODE_OPTIONS