Not strictly a fix, but there was this related thread that was more or less counteracting the limits of the file structure breaking updating, with duplicates appearing
What’s worse for me is that for say, Cave Story, I modify the action file to point to a different core directory. Instead of being just duplicated, it gets overwritten.
I just posted something to the main 0.5 thread, pertaining to a bug in the file structure and very much related to duplicate locations causing problems.