ZDoom

The file in question should not be part of the distribution because it is auto-generated. So it seems the only way to fix it is to be more careful while packing things together. This isn't something that can be fixed in the project itself because the file isn't part of it. It's just being created in a directory that gets packed into the distribution package so apparently it's too easy to add by accident.

Looks like someone broke Linux compatibility in wadsrc/wadsrc.

On the last line, it says to run the command "..\tools\makewad\makewad.EXE" which we all know isin't valid in Linux,

Simply changing the '\\'s to '/' and removing the .EXE fixes it. I'm sure you could do some kind if ifdef thing for it since it worked before.

(actually, upon further reasearch, it was the Linux way anyway before. Makes sense since the VC version doesn't use makefiles)