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
I removed these files, their Bio.motifs siblings are being tested
Fix strange type checking in NeuralNetwork code
Fix strange type checking idiom
Suggestions from $ 2to3 --no-diffs -n -w -f idioms Tests Doc Scripts
Suggestions from $ 2to3 --no-diffs -n -w -f idioms Bio
Silence SFF indexing test warning for .diy dummy index
Suggestions from $ 2to3 --no-diffs -n -w -f next Tests Doc Scripts
Selected changes from $ 2to3 --no-diffs -n -w -f next Bio

I have not included changes of the 'next' method on
our objects to '__next__' since that changes the API
and may break things... this issue needs more review.
Applying next idiom fixes to the Tutorial examples
Change suggested by $ 2to3 --no-diffs -n -w -f tuple_params Bio BioSQL Tests Doc Scripts
Change based on suggestion by 2to3 types fixer
Changes suggested by 2to3 zip fixer
Workaround for Python 2to3 bug http://bugs.python.org/issue19111 and zip import
Update a comment about zip (iterator in Python 3)