Default constructor should be ok in these cases.

Especially when printing size_t it is better to use << operator
which always uses the right size.

`except:` might catch the wrong exception by mistake

[makedoc]

close #450

this allows parsing the plumed input file by setting the number of atoms without the need of reading a trajectory file
DRIVER does plumed initialisation and then stops

@all this is meant for the plumed-nest, please have a look and comment

@chi2, @chi3, @chi4 and @chi5

now an option to avoid clearDependecies.
This allows to have in a single class actionAtomistic and actionWithArguments
and actually use them together

this is used in Action build on MetainferenceBase where requestAtomst(atoms, false)