That actually opens a REPL on your open IDE instance. I use it for developing and it's occasionally useful for support debugging too. It's usually hidden behind the idea.is.internal flag, which I guess you have on for plugin development.
Relatedly, I have seen your Github issue, and my apologies for taking so long to reply. I meant to update my website with the information but got sidetracked and haven't done that yet. The TL;DR is that I don't recommend using Clojure, I recommend Kotlin since it's by far the best-trodden path and also doesn't suffer from the classloader issues you're experiencing or other problems that Clojure suffers from in this context.