I made a few more changes to setup.py in order to work with MacPorts.
This allowed me to add a temporary Portfile for py-plumed
that is now used in travis tests.

The plan is to submit this Portfile to MacPorts after we release v2.5

Notice that one test is duplicated (python/test) in order to be available
when using nosetests from python.

The old analysis class was reaching a stage where it was not fit
for purpose.  This is thus a total redesign in order to allow us
to write better algorithms for dimensionality reduction that are
flexible and easy for users to use.  I have removed some functionality
with this commit but I will re add it in subsequent commits
Also added information on analysis classes to developer documentation

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

This test shows a problem in reweighting (discussed in #48).
In particular, histoA and histoB in this regtest should not
come out identical as they do.