cc: @gtribello

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

[makedoc]

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

Year in header is here updated to 2017

[makedoc]

Addresses #226

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

Notice that as of now it is not fully integrated in the plumed
reference/ module. However, it is possible to compute
ERMSD from a given structure and to use it as a CV

[makedoc]

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

Allows to specify residues with chain id as letter, e.g.
phi-A102

No letter implies first chain

Fix #133

There were some problems with the documentation generation in SPRINT
that are now fixed.  Some routines in MultiReferenceBase were not in
a very sensible place.  I also changed PDB so that you can add stuff
to the remarks.

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

The nature of the backbone is now specified by a class called MolDataClass.
A warning is given about GLY residues

This involved splitting the code for reading an argument list from the code
for interpretting it, adding a function for reading the ARG argument from the pdb and
interpretting things like ARG=d1.* to ActionWithArgument and adding a routine
to PDB which allows you to replace the old ARG=d1.* with the newly interpretted
ARG=d1.x,d1.y,d1.z