Take a look at version 2.1.2.1 (on the download page).
We now have something called "group collection". You can't create collections of collections, but you can create collections of groups.
It was a several days of work to implement it and there are probably some small bugs in the editor still. There are so many possible combinations of drag, drop, copy, paste, insert, etc. to keep track of. Other parts of the program had to be updated as well, but hopefully everything else will behave as before.
Pay attention to the new icons in the editor as well.
Empty groups will not be loaded at runtime. I think the error you were getting was actually because of the way you were naming the groups, with no valid filename characters. A file is created for each group to store the compiled grammars. But anyway since it won't try to process an empty group you can name it whatever you want now, even just: ________________________
