Currently, all the OneJS UI scripts you'd write are inside of your project's
persistentDataPath. While this setup works well for Editor and Standalone builds, it does mean you'd need to keep 2 repos (one for UI and one for your Unity project) or deal with the script packaging and extraction yourself.
So this workflow is being re-worked right now to allow you to keep your OneJS scripts under your project's root (same level as your Assets and Library folders) so you can keep everything in just 1 repo. An automatic script packager for your standalone build will also be included. Expect all this to land fairly soon.