after 18b63365

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

Year in header is here updated to 2017

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

See #200

See #200

Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

MultiDomain allows you to calculate the RMSD separation
between multiple separately aligned parts of a configuration
at once.  Changes to all the files were to put some sanity
checks in the code to hopefully make it easier to debug the
applications of the tools in the reference module.

Changes were also needed as this feature was broken as a consequence
of changes in no-buffer branch.  Change to dynamic list deletes
a check that is active when you compile with -DNDEBUG that is not really needed

initialization list

To do this I had to make requestArguments in ActionWithArguments
a const method is this a problem?

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