Resource loader doesn't load assets from source sets apart from main in dev. This causes issues with annotation processors that generate resources, as they output into the default source set (at least under Eclipse.) This appears to be caused by the resources being loaded from the filesystem rather than from the classpath.

With the newer Fabric Loader versions, it is now possible to specify multiple paths for a specific mod, so you can add extra paths for the additional resource folders.

Do you have a simple test case to reproduce this?

Not exactly, considering there doesn't really exist such a thing as a non-complex annotation processor. Will try to clean up a bit of the awful code in mine and upload it, though.

Uploaded my annotation processor that can be used to reproduce this issue here. The code that actually utilizes it looks something like this:

@RegistryContainer("modid", blockModel = BlockModelAction.BASIC_BLOCK)
public class Init implements ModInitializer {
@RegisterBlock("test")
public static final Block Test = ...

public void onInitialize() {InitRegistrar.register();}
}

(InitRegistrar is also generated by the annotation processor.)