*bump*
I have the same issue when trying to use any mod from the example repo (like unit_features), or make a new mod from scratch. No errors, but none of the changes apply. Making the same changes to the base game files works perfectly, but the mod system doesn't seem to do anything.
(I'm also running on Linux, where paths are case sensitive, and the manifest seems to convert all paths to lower case - but it also fails when the files I edit only have lower case names).

Quick and dirty workaround: I wrote a short python script that will mix and match symlinks to mod and game files in the game dir. Should work for pretty much any game, not just RR (as long as your OS handles symlinks properly; Linux does, Windows might).
https://github.com/APfeuffer/Modmerge