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The Bundler component (on ScriptEngine) takes care of bundling your scripts at buildtime and extracting the bundle during runtime.

You can configure where your scripts should reside under ScriptEngine's MISC section (via the Editor & Player WorkingDir properties).

The bundling and extraction process is fairly automatic so you don't need to worry about it too much.

Live Reload, on or off

For production deployment where you don't need Live Reload, remember to turn it off by unchecking the "Turn On For Standalone" option on the Live Reload component. By default, this option is on because during development you may still find Live Reload useful for Standalone builds/apps.

link.xml for AOT Platforms and IL2CPP

AOT Platforms and IL2CPP builds will strip all your unused C# code. So for all the classes you'd like to call dynamically from Javascript, you'd need to preserve them. link.xml will do the job. Here's an example:

    <assembly fullname="mscorlib" preserve="all" />
    <assembly fullname="OneJS" preserve="all" />
    <assembly fullname="UnityEngine.CoreModule" preserve="all" />
    <assembly fullname="UnityEngine.PhysicsModule" preserve="all" />
    <assembly fullname="UnityEngine.TextRenderingModule" preserve="all" />
    <assembly fullname="UnityEngine.UIElementsModule" preserve="all" />
    <assembly fullname="UnityEngine.IMGUIModule" preserve="all" />
    <assembly fullname="Unity.Mathematics" preserve="all" />