Move -debug to cmdlinemodulemanager.cpp

Move -debug to cmdlinemodulemanager.cpp

Now the option can be used uniformly even for tools that do not call
parse_common_args().  The description is still mdrun-specific, though.
While at it, made it work without an explicit debug level: if only
-debug is provided without any value, the debug level defaults to 1.
Also made -hidden work for 'gmx -h', as there now is a hidden option
there.

Renamed some associated functions to start with a gmx_ prefix, and
reorder things in fatalerror.* so that debugging code is in a single
block, and functions are in the same order in both files.

Removed unused debug_level from oenv.  This probably needs a better
mechanism to control what is written to the debugging output.

Change-Id: I1526916356b545c56d9f601f121e6c4e581639eb