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

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

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

Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

This is so we can deal with the fact that derivatives can now
be added to other multicolvar centers even when you are working
with regular multicolvars.  This is again getting us towards
having a list of multicolvar objects that changes dynamically

The idea here is to move towards multicolvar CVs such as the Q4 parameter
for those water molecules that are forming 4 hydrogen bonds.  We will have
that the input to any multicolvar can itself be a multicolvar which would allow
things like this to be computed using a multicolvar filter

Chnages were made in a number of places to (a) ensure that this
functionality was available in a large number of multicolvars and
(b) to prevent duplication of functionality between the new vessels
for the maximum and minimum and the old colvars for calculating functions
of all the multicolvars

The new multicolvar measures the inplanedistance i.e. the
distane from a plane defined by a vector connecting two atoms.
The new refernce distance measures the dot product distance
between two points