Fix str2bool to account for integer encoding of booleans

Some Phyloxml files use 0 or 1 for true/false
Merge pull request #239 from evolvedmicrobe/master

Fix str2bool to account for integer encoding of booleans
Close #206: greytrack_font_rotation is linear only
Remove accidentally committed file

Note this checked in file had an unfortunate typo, XY vs XZ,
and for more background on random access to blocked XZ format
see my blog post here:
http://blastedbio.blogspot.co.uk/2013/04/random-access-to-blocked-xz-format-bxzf.html

See also my backport of the lzma module which this used,
https://github.com/peterjc/backports.lzma
http://pypi.python.org/pypi/backports.lzma/
Downgrade more non-null SFF padding errors to warnings (issue #219)

Based on a patch from Martin Mokrejs submitted by email.

See earlier commit, this is to allow Biopython to parse the
invalid SFF files generated by sff-dump.2.1.7 though 2.1.9
due to bug reusing a buffer resulting in non-null padding.
Downgrade remaining SFF null-padding errors, issue #219
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.