I already have a diff-merge for doing it. The point is I really shouldn't need one. It is possible that Toady is already checking for multiple files in the init folder...actually it is probable. I haven't tested yet to see if it is the case.
No matter what I would like to have the directory structure changed so that user data is seperated from the game data. Moving the save, movies, and init folders up to the df level covers most of the user data. Moving the art folder from data to raw, finishes it.
These changes make upgrading a matter of deleting the data branch and unzipping with overwrite. Instead of unzip, then copy and edit all the stuff I have into the new.
This could be further extended for modders by making a naming convention on the raws, such that item_food.txt is done, then item_food1.txt, item_food2.txt, etc. Tags in the numbered files would override those in the default file, and the object file would be built as a total of those files.
It is just one of those polish type things that makes it easier for users. It also could eliminate the 5 to 10 bug reports that appear every version from someone leaving the object files around from a previous version. Easy changes for Toady to make, that give a large benefit.