Reading about manifests immediately reminded be of Clearcase/Clearmake. My memory may be not correct after all the years passed, but configuration records for derived objects contained the same information as proposed manifests + some more metadata about source (versions, at least). If I remember correctly SCons allows to implement a custom "checker" (or whatever it is called there) to compare files based on any criteria that are useful, not just timestamps. But this is about the only visible advantage of SCons over Make, at least for our case.