Multiple non-conflicting mods

[Marshall]

An interesting point DCoder,

At present, I don't actually know how to launch RA2MD.exe and then wait for GAMEMD.exe to close, although I can probably figure such a thing out.
As for what to do in the event the files are not restored, your suggestion seems like a good way to go. If the program stores removed files in it's own backup folder, then on launch of the program it will detect that these files are present and restore them then. Such an event should of course be documented in the program's documentation.

Patched files are more tricky, because I don't know what files are patched. So far for the Clean Up program, I have assumed that langmd.mix is the only file modified and is only modified by DeeZire AND an appropriate backup exists. I would probably go on the same assumptions here.
The only other patched file I am aware of is gamemd.exe. I am hoping to have this program replace the Rock Patch installer, by having users only download the latest patch file and letting the Mod Manager control whether or not the Rock Patch is installed. [I will also write a small program for pd to generate the patch file so that he can upload it without having to wait for me to generate the installer.]