Removed a debugging flag that was resulting in unnecessary overheads in
sequence-only mode.
Fixed a few bugs that seem to have arisen from a previous commit having
been deleted due to a forced update.
Re-added option for fixing minimum epsilon, which was lost from a
previous commit.
Added option for enabling printing of logging information during the
burnin, and also fixed a minor bug with the printing of the likelihood
in the log file.
In StructTrace.java, re-enabled printing of final rotations and
translations without DEBUG flag.  Might want to have these available
creation of figures.
Fixed printing of log info during burnin.
Merge branch 'structalign' of ssh://github.com/statalign/statalign into structalign

Merging changes.
Added labelling to internal nodes.
Fixed obscure bug whereby internal node labels were only printed during
the burnin.
Restored topology move tuning parameter to its previous value.
Math.exp -> FastMath.exp inside Utils.logAdd reduces runtime by 5
percent!
Resolved some issues with the hierarchical prior formulation which meant
that previously the priors were slightly different from what was
intended.
Merge branch 'structalign' of ssh://github.com/statalign/statalign into structalign
Changed default prior for sigma2 in hierarchical formulation to uniform
(still proper, given the form of the parent prior).
Changed back to global-sigma default.
Changed default prior on nu to match what it was previously.
Fixed typo whereby two tabs were being inserted into alignment sections
of the log file, which conflicted with the format in previous versions
of StatAlign (which contained only one tab), making certain downstream
post-processing tools throw errors.
Changed hierarchical prior formulation for local sigmas to LogNormal
rather than Gamma.

Deactivated RNA mode by default on RNA sequences.

Switched off auto-tuning for substitution moves (was not actually
implemented in any case).

Changed some of the default prior hyperparameters.
Implemented localEpsilon mode, whereby B-factor information provided as
an optional fourth column in the .coor file is used to weight the
contribution of epsilon on a per-site basis. This helps account for
differential flexibility and uncertainty at different regions of the
structure. The cost is an increase in runtime of ~2 fold, since the
covariance matrix is now different for each column, and the Cholesky
decompositions cannot be cached.
If any structures contain all zeros for the B-factors, they are now
replaced with ones.