Turn on -Wunused-parameter where applicable

Turn on -Wunused-parameter where applicable

There are no longer any function parameters that have function
arguments that are unused (under at least some code paths), unless
they are so noted with gmx_unused attributes. This commit activates
the applicable compiler warnings, so that we can keep it that way!

Some extra changes in gmxomp.c to satisfy Doxygen and remove unused
variable warnings as well (moved the file to C++ compilation).
As a side effect, simplify the #ifdef logic.  The only visible effect of
the reorganization should be that if both affinity environment variables
are set, then the warnings get printed in reverse order.

Also run uncrustify and copyright on changed files.

Change-Id: Ifbaba7543f30c94b44b649718c0c5d7ff1fe5db0