Fixes to free energy code, output & g_bar compatibility.

Fixes to free energy code, output & g_bar compatibility.

- Fixes to the handling of the new free energy input options, so that
    input are more stringently checked and common errors are caught.
- Fixed g_bar so it can deal with output from mdrun (in dhdl.xvg and
    ener.edr input)
- Free energy output is now backward compatible with g_bar if 4.5-style
    settings are used
- Some mdp option documentation clarifications.

This fixes issue #1090

Still left to do:
- g_energy -odh relies on an ugly hack to get the xvg headers for free
  energy
output to work. That needs to be fixed so ener.edr can be interpreted
independently from the associated tpr file.
- The mdp documentation could use some more improvements.

Change-Id: I6198f935a94b7341d8dd85444e348ea8a55621ad