Remove duplicated copies of motif application wrappers

The code is still identical, so we can point Bio.Motif.Applications
at the replacements in Bio.motifs.applications instead. This is
easier because I'm about to fix some property names in the XXmotif
wrapper and only want to do it once.
Property checking wasn't strict enough in Application wrappers

This allowed some issues with the XXmotif wrapper to be committed,
see next commit which addresses this.
Fix invalid property/argument names in XXmotif wrapper.

We can't use minus signs as hyphens in Python properties
or argument names (which the application wrapper code was
not checking properly until the last commit), switched to
underscores.

I also switched to lower case names rather than all capitals
to make them PEP8 compliant.

These changes do break back-compatibility but I believe this
slight pain is worth it. The old ALLCAPS names remain as
aliases for use via the set_parameter style.

See mailing list thread:
http://lists.open-bio.org/pipermail/biopython-dev/2013-August/010767.html
Add an application wrapper and unit test for the MSAProbs alignment software.
Minor corrections now the application wrapper code is stricter
Thank Christian Brueffer in NEWS for MSAProbs wrapper