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

[makedoc]

(cherry picked from commit 781e5677)

[makedoc]

see 8ed9697a

Can be found with the following python snippet

import re
plumedDictionary={}
with open("/opt/local/lib/plumed/vim/syntax/plumed.vim") as fin:
    for line in fin:
        if re.match("^let b:plumedDictionary\[.*$",line):
            line=re.sub("^let b:","",line)
            exec(line,{'__builtins__': None},{'plumedDictionary':plumedDictionary})
for key in plumedDictionary.keys():
    diction={}
    for opt in plumedDictionary[key]:
        if(opt['word'] in diction):
            print(key,opt['word'])
        diction[opt['word']]=1

I think this is more robust. If an MD code uses a negative value with a
specific meaning (e.g. -1 to imply some choice) casting to unsigned
will translate -1 to 4294967295, which is positive

This fixes #446

Requires adding a cpp-suppress