More binaries into the wrapper binary.

Move most remaining binaries to be built into the 'gmx' wrapper binary.
Now, only mdrun and g_pme_error (which have a different initialization
sequence), and ngmx (and other X11 programs) remain outside.

Renamed a few headers to match the name of their implementation file.

Part of #685.

Change-Id: I3fb7e3de905c01d7564d809893390bbb9b8f8368