cc: @valsson

cc: @gtribello

The used modules were not detected correctly on travis probably due to
some settings for the cd option. This was harmless since the list of used
modules was not checked indeed.

required fixing some incorrect escape sequence in plumedcheck

closing files to avoid too many open files

- Allow Plumed objects to be explicitly finalized
(can be used to make sure files are closed correctly)
- Allow Plumed objects to be used in context managers

Solves a bug with METAD + TARGET + GRID_SPARSE
See also #467

should be not important. In particular, when invsigma was <10-12
sigma was set as equal to invsigma. Now it is set to zero,
which I think is the expected behavior.

I verified it, I will then modified a regtest so to keep checking for this

python module should always be called `plumed`, irrespectively of
prefix/suffix. Notice that if installing multiple plumed versions
side by side different python modules will anyway end up in different
directories (`lib/program_name`).

Function was very slow when variables were not present or had zero derivative

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

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)

See #435