[makedoc]

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

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