Ok, think I got something.
One thing I didn't realize to mention is that nowadays files should be referenced without path, e.g. model xml-files inside weapon specification files just with the filename. This practically enables applying overlay mods as intended.
E.g. in mp40s\weapons\BAR.xml:
Code:
<model filename="media\models\bar.xml" />
--> change to
<model filename="bar.xml" />
Once these are fixed (I fixed only the first four of them to test), there's another issue. As folders don't have any meaning once the files end up in the resource management system, unintentional name clashes might happen, so watch out for that. It seems that Ogre's resource system is case insensitive, or at least I have it that way in RWR, so weapons\BAR.xml may actually end up overlaying (overriding) models\bar.xml, and the loader goes berserk finding a weapon specification file when it was trying to find a model file, or vice versa.
To fix it, I'd suggest you to change the .xml extension in all files in weapons\ to .weapon, and update whole_stuff.xml contents accordingly. Changing the voxel model -xml extension doesn't seem to be an option right now, I've got a check for it in the code, although it shouldn't really be needed.