- dumpgrid
- pca
- mds

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

There are now fewer warnings when Doxygen runs

Also fixed how weights are dealt with in analysis and mapping
weights were stored in different places in analysis and mapping
this was confusing for developers.  The weights are now always
inside the individual ReferenceConfiguration objects