Fixed GMXRC so we are not polluting standard shell variables

csh/tcsh is now detected by looking for the lower-case $shell
variable, which seems to work on all recent platforms, instead
of using the 'set' command (which affected $* and $@ in bash).
Fixes #1044.

Change-Id: I852d075c80e2bf8f81a02932432dd31b3bab7f09
Merge "Fixed GMXRC so we are not polluting standard shell variables" into release-4-6