When you execute CMake, if you add -G Ninja for using ninja instead of GNU Make, this error is printed on the console:

CMake Error:
  Running

   '/usr/bin/ninja.exe' '-C' '/home/carlo/z' '-t' 'recompact'

  failed with:

   ninja: error: build.ninja:4847: multiple rules generate src/Plugin/AlienWah/libZynAlienWah.dll.a

Perhaps, this happens because this line:

and this line:

have the same output name. The same effect could be seen on other plugins.
I tested this issue on CYGWIN and MinGW, but I think it should be possible to reproduce it also on Linux.

EDIT: tested on Debian, CMake completed the configuration process successfully and it didn't raise the error that happens on Windows.