Merge branch 'merging-plumed-file-tool'

This is a very big commit on the master branch. The way plumed write files (such as COLVAR/HILLS /etc) has been completely changed. We now have:
* automatic tagging of the columns with an initial "#!FIELD" line
* automatic backup when trying to overwrite files (a la gromacs)
* restart is driven by a standalone line "RESTART" in the input file, which activate restart for all the other keywords.
This may affect quite a bit the behavior of plumed. A few examples:
* If you use metadynamics, HILLS format is slightly changed (there are tags now). Have a look at one of the newly produced HILLS file
* COLVAR files are not anymore appended by default: you have to specify RESTART (on a separate line)
* unpredicted bugs may have been introduced!