I assume you mean that it stops ~compiling~ when working through the archive manager. There’s no way to build just the executeables you want without building the underlying libraries. We’re making the libraries less tightly linked together as we go (and a dependency of InterativeAbinitio on ArchiveBase is likely to be considered a problem, once we get as far as protocols).
Go ahead and continue commenting out files that won’t compile (IterativeAbrelax.hh/cc, etc). Let me know what your total list is and I’ll tell you if you should be worried.
You can also trying dummying out functions in the archive manager by deleting the guts of functions bodies in the cc file it fails on and replacing them with something simple (return, or return followed by a constructor for whatever variable it’s supposed to return ought to work).
I can’t reproduce your error or I’d give you a patch that will fix it…