Added a comment.
Added automatic tuning for rotation, translation and library moves.
Library seems to be always rejected though.
Corrected a typo.
Print statements.
Changes to move weights.
Removed a duplicate function at the end of StructAlign.java.

Fixed a non-initialised array problem for the non-global sigma case.

Fixed the inclusion of the prior densities for the parameters --
previously we were essentially assuming a uniform prior for everything.

Also, added additional prior types (hyperbolic and inverse gamma), and
assigned these to the parameters as appropriate.

Epsilon now has an informative prior, with mode at 1, and inference
seems to be better on this parameter now.

It is now also possible to switch between different proposal schemes
very easily. Currently implemented are Gaussian random walks
(GaussianProposal) and the original Gamma random walk (GammaProposal).

As well as making the code more readable and maintainable, these
modifications should make adding new ModelExtension types easier, since
the generic MCMC framework is already there.
Conflicts resolved.