Okay this is the kind of issue that will make me abandon a product. 
I create files in a specific folder
I add them to my project in AppCode and... it MOVES them!
I spent several hours yesterday puzzling over why the hell i was generating new versions of the files, and they were right on disk, but when I went back to AppCode they were wrong. Of course eventually I figured out that AppCode had moved the files somewhere else without my noticing. So the versions I was editing were not the same as the versions I was generating.
I didn't ask AppCode to move them, I don't want it to move them. I put those files there for a reason. I am now using Xcode to add files to my projects again.
This is unbelievably annoying.
 yes this is hyperbole but just take it as a sign of how angry i was when i realised what AppCode was doing.