cppcheck warnings

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

Also tidied up how STRIDE and USE_ALL_DATA works for analysis
objects.  Now everything works in a manner similar to GRID

I also fixed made the data collecting class is aware if we are calculating
a distance.  If it knows that we are trying to calculate a distnace
it returns something with which it can calculate a distance and not
the position stored by COLLECT_FRAMES.  I am not sure this is necessary
and if it will be ever used but I guess it is better to be safe than
sorry

You can now use COLLECT_FRAMES to collect pdb data from the trajectory
and output a pdb file that contains the underlying atomic coordinates
in pdb format even if you are not using the rmsd distance to measure
the dissimilarity matrix for dimensionality reduction.  Also fixed
a number of bugs.

The data is now passed via a pdb object.  This means we can now use
the same infractructure for setting up the ReferenceConfiguration as
we use in setting up the ReferenceConfigurations in paths and so on.
Projections meanwhile are attached to the ReferenceConfigurations
when they are required for printing.  So now a reference configuration
can be the pair of objects - i.e. the projections and the high dimensional
configuration.

I have moved mds from the analysis module to a separate dimred module
as I think it is best to keep this with the other dimensionality
reduction algorithms.  It is now default off though