set stage->inputs properly (I think), plus debug/comment updates
-rw-r--r-- 55449 Make-config
-rw-r--r-- 32076 Makefile.X11
drwxr-xr-x - bin
drwxr-xr-x - docs
drwxr-xr-x - doxygen
drwxr-xr-x - include
drwxr-xr-x - progs
drwxr-xr-x - src