These are X11 keyboard mapping files for HHKB (and some other models of keyboards).
0-9
and !@#$%^&*()
are swapped in the "prog" version.
unix> xmodmap ./.Xmodmap
unix> xmodmap ./.Xmodmap_prog
It would be more convenient if you change some keyboard shortcuts.
For example:
Ctrl + Alt + A -> xmodmap ~/.Xmodmap
Ctrl + Alt + S -> xmodmap ~/.Xmodmap_prog
Alt + 4 -> Alt + F4
...