Model "replacing" compilation flags explicitly

We currently model flag changes as either "add" or "delete". "Replace" happens e.g. for profile file locations - is better modeled explicitly, rather than a delete followed by an add, because it allows catching setup errors where, say, a profile was meant to be used during compilation, but the experimenter forgets to pass one. Removing and not adding the flag _will_ work - compilation will just chug along - but the results will be garbage, and hard to tell why. Expressing as "replace" would mean "we expect it to be present in the compilation, and a replacement provided, so if that's not the case -> error"