Clean up genbox and associated code

Clean up genbox and associated code

Moved genbox utility to preprocessing module from analysis module.
Renamed its addconf implementation files. Fixed necessary #include
dependencies. Made several functions static.

Renamed gbutil.[ch] to conformation-utilities.[ch], because they are
not exclusive to anything abbreviated "gb." These are mostly used by
gmxpreprocess, but also mdlib/tpi.c, and the header file is not really
useful to install, so the only current place they should move is
gmxlib. Removed unused orient(). Renamed genconf() and gen_box() to
avoid confusion with the utilities of those names. Moved the new
make_new_conformation into genbox.cpp because it is only used there.
Made two functions static. Removed unused (maybe broken?) NTB
parameter of the new make_new_box() function. Removed some debug
code that used a print function in a different compilation unit.

Change-Id: I33d15b2df63c9422ce241782a922145f4626b0fb