Every time I’ve used the new jucer so far, it made me the build structure, then I stayed in xcode (just targetting Mac & iOS - in fact I mainly used it to get an iOS project going.)
But I’m concerned about changes I make to xcode and what will happen when I go back and forth. Obviously file adds should be in the jucer, and in theory, all files should be common (I had some problems getting includes and platform compiler vars included early enough to make that work well, but obviously it can work), but iOS needs some project specific xcode settings, notably connected to code signing and decode versus distribution provision profiles and other Apple silliness (some of which are developer specific).
Can jucer add files and make other useful changes without affecting that stuff? It would obviously be sub-optimal to have to add all files before any developing is done, or to have to reset all the xcode stuff every time a file is added.