Now I wonder (not that much of an issue to me. Since to my own JCR6 system that I use in nearly all my projects, this error won't hit me (good thing, as my project would exceed 1000 files otherwise already)), but why this limit anyway? Now the question by That Other Fish, makes me think it could indeed be because there could be too many files to find the main executable, and then indeed I wonder if files in sub-folders are indeed fine.... ;)
Viewing post in "Too many files in zip" error
It's not hard to find the main file, since it has to be named index.html and nothing else. The issue is twofold: one, a safety limit that prevents someone from e.g. uploading a zip bomb and causing a DoS on the server side, and two, a common sense limit so players don't find their own browser and OS taken out by a game too big to load and play. It happens often enough to me as it is, with games way under the limit.