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

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

(style) warnings

[makedoc]

Also had to avoid using vector.clear with a std::vector<Vector> as
the code complains when the code is compiled with g++ and more
excessive debug options