Ok, I've been working, and I've copied the atomic invoke, which-os, make-directory and make-directory* , and datetbl fixes from ac.scm.
That resolves the most recent issues, but I've been looking through the code in ac.scm and arc-exe.scm and there are still major differences. For example, while looking at the change from * call* to call*, I found that arc-exe.scm never got the defcall change in the first place. So keeping arc-exe.scm compatible with ac.scm is not just an issue of changes from now on, because the two files are already somewhat divergent.
On the other hand, if we got arc-exe.scm to just load ac.scm somehow, we wouldn't have to worry about all this. Unfornately this may not be easy; I threw myself at the problem for a couple of hours and didn't really come up with anything, except for a severe dislike for scheme's module system.