Monolith, it kind of depends on what is getting swapped around.
In the case of whole files, some of the dependancies might be "real," meaning that one file is required because it points to another that is changed. Ie: if you use a folder with minesweeper changes I made and you don't change the Roster you'll CTD because I change the unit type from 5 to 1, and it's in both files.
Most are not so complicated and messy.
In the case of the ini, dat, sim, etc files, THAT is where it gets messy. You not only need to know what file was changed, but HOW it was changed. Like if you want a certain visual effect from one mod, but the sea etc from ROW, you might have to open up files with a tweaker or S3D and add in the stuff you want. That's really what I meant by "complicated."
tater