Test case for bytes/unicode issue with Entrez.epost under Python 3

Reported on the mailing list by Nicolas Joannin
http://lists.open-bio.org/pipermail/biopython/2013-January/008307.html
http://lists.open-bio.org/pipermail/biopython/2013-March/008430.html
Fix Python 3 bytes/unicode issue with Entrez.epost

Based on fix from Nicolas Joannin on the mailing list,
http://lists.open-bio.org/pipermail/biopython/2013-March/008419.html
Skip test_Entrez_online.py under Jython
Make Jython DTD parsing check specific (in case they fix this)
Merging the Biopython Structural Bioinformatics FAQ into the main documentation. This still needs lots of work, but at least all the information is in there somewhere.
Merge branch 'master' of github.com:biopython/biopython
Making some progress cleaning up the PDB chapter
Issue a warning when translating partial codons

See mailing list dicussion. Some felt this was useful functionality
and perhaps worthy of another optional argument to the translate
functions/methods, but they are already quite complicated. Using
a warning for now, and an exception later is to help migrate old
code which may be using this (e.g. ORF finding code).

This will requires explicitly padding/trimming the sequence to be
a multiple of three before translation.
Avoid new translation warning in unittests
Ensure ORF finder translates no partial codons.

This is to avoid the new warning message if translating
a partial codon.
Avoid warning from partial codon translation
Truncate test sequences to avoid partial codon translation warning
Avoid partial codons and new warning
Make the new warning fixed text for ease of filtering.

Old version include the sequence length, making a simple
filter based on the message and warning type impossible.
More progress on the Bio.PDB chapter
some further progress on the Bio.PDB documentation. Not donen yet, though
Finished merging the Bio.PDB chapter in the Tutorial with the Bio.PDB FAQ
AlignIO now interleaves (wraps) large Nexus alignments to avoid long lines.

This should allow it to be used with MrBayes, while continuing to
output non-interleaved Nexus for smaller alignments where there
have been no issues reported. See mailing list dicussions:
http://lists.open-bio.org/pipermail/biopython-dev/2010-December/008487.html
http://lists.open-bio.org/pipermail/biopython/2013-March/008457.html
Test command line wrapper handling of stdout/stderr
Must open /dev/null for writing.

Very curious that this didn't cause a problem with stdout,
just stderr. Thank you to Lenna and Saket for spotting this
http://lists.open-bio.org/pipermail/biopython-dev/2013-March/010488.html

Finding and fixing this unreported bug was a nice bonus from
writing test_Application.py :)