Adding ``timeInSubsPerSite`` option.

Adding option to scale time in expected substitutions per site.
Updating code to accommodate a ``timeInSubsPerSite`` option in the
config file which defaults to 0 (false), but if not zero (true), causes
time to be in expected subs per site. This required changes to:

    dpp-msbayes.pl
    msprior.c
    msprior.h
    setup.c

Most of the changes were required to handle the new option. The changing
of the time scale was as simple as setting ``meanTheta`` to 1.0.
Updating old model.

Making some changes to the following files in the ``old-model``
directory:

    msbayes.pl
    msprior.c
    setup.c

Making three changes:

1.  Rescaling time using the mean of the uniform prior on theta (rather
    than half of the upper limit). This now mirrors the dpp code.

2.  As I did for ``dpp-msprior``, I am updating the hack where there was
    a check for small (i.e., 0.0001) divergence times. In such
    simulations, the div time was set to this arbitrary lower bound, and
    the bottleneck time was set to 0.5 of this.  I am guessing this was
    to prevent unrealistic (and numerically unstable?) changes in pop
    size. However, 0.0001 can be thousands of generations which is not
    trivial. Also, rather than this weird hack of the bottleneck time,
    it seems much better to simply have no bottleneck if the div time is
    essentially zero.  Accordingly, I lowered the threshold and simply
    "turn off" the bottleneck if the time is below it (I no longer
    adjust the div time or bottleneck time).

3.  Adding support for ``timeInSubsPerSite`` option, as I did for the
    dpp code. This boolean option in the config allows the user to have
    time in the scale of expected substitutions per site.
Fixing errors in ``old-model``.

Fixing errors in ``old-model`` that were introduced with the addition of
the ``timeInSubsPerSite`` option. I forgot to declare the variables for
the new option in ``old-model/msprior.h``. These are now added. I also
deleted a curly brace on line 382 when I added the new option to the
``SetDefaultParams`` option. This has been added back in.
Merge branch 'timescale' into dev

Merging work on the addition of ``timeInSubsPerSite`` frome the
'timescale' branch into the dev branch.