I went through cppcheck warnings (style) and fixes those I understood.
Mostly issues related to scope of variables.

This commit contains changes automatically generated by plumedbot on Travis-ci.

macports ccache was not saved correctly

Fixed partial_tempering with gromacs 5 convention. Old behavior can be
forced with --gromacs4 option.

added comment in config.txt file

Two bug fixes for VES module

Fixed conflict in changelog

make clean was not correctly cleaning plumed executable

Thanks to Qingh Liao

correct definition of G vector in the documentation. A 1/gamma factor was missing. The actual calculation was correct and it remained unchanged.