can I use kapt to run java annotation processors over java source code only? when I am trying to do this I always get:

[WARNING] No sources found skipping Kotlin compile

No, it will abort when there are no Kotlin sources. But you can just pass an empty Kotlin source file. I do that in my kotlin-compile-testing library

that could be an option, but I would say this case must be supported

Perhaps it's possible somehow. But I didn't bother since this hack works perfectly well. There are experimental Java options for the compiler that might work, but in my experience those are very buggy.

Maybe better would be use apt if you have Java only sources in some modules, it would be also faster

in fact I would like to have it unified, and I also tweaked kapt a bit, hope it will be merged at some point

Tweaked kapt? I think faster builds (especially slowest part of the build) worth a lot more than unified config

for my case not, I would not like to migrate each subproject in my company one by one