Updated some .mdp file variables to use "-" instead of deprecated "_"
In the .mdp file, now a minus sign instead of an underline is
generally used. Some sections of the manual still listed .mdp
variable names in the old notation.
- three manual sections (pulling, enforced rotation and computational
electrophysiology) now use "-" instead of "_" in .mdp file variable
names
- updated output of rotation code to reflect this up-to-date notation
- no functional changes are in this patch
Change-Id: I7b00193d3e3d549ce8c9a728b307280c0bdd35ce