Justoverclock I think that's normal, it shouldn't prevent you from compiling the code with npm run dev. You can run the npm commands in a separate terminal or using the built-in terminal in phpStorm. In my streams I always have a second terminal window open with the npm command.
In Flarum beta 16 you can now install the flarum npm package that provides type-hinting for those "modules" for the imports that phpStorm otherwise cannot understand. I think I might have shown how to install that (optional) package in the latest streams. If you make your extension with the extension generator the typings should be installed out of the box.
Even with the typings package, phpStorm isn't fully able to type-hint everything on the javascript side. It's very good on the PHP side, less so on the javascript side. But it's mostly because Flarum typings are not perfect yet so phpStorm has just no clue. But it won't prevent you from typing code, it might just underline some things and tell you it can't verify they are valid for you.
