Tweak doctest for Jython 2.7b2 and 2.7b3

See http://bugs.jython.org/issue2007 (not the first time
we've had to avoid this Jython 2.7 beta X bug).
Minor docstring tweaks
Close handles in test_Entrez_online.py
Check URLs in test_Entrez_online.py
Fix test_Entrez_online.py changes on Python 3 etc.

Can't use simple URL string matching as the parameter order changes
between Python versions as it is built from a dict.

(Was meant to be part of previous commit)
Update EvilHandleHack to preserve any URL attribute
Add test for issue #361, repeated IDs in elink
Phylo.root_with_outgroup: updated a comment on Py3 compatibility/hack
Phylo.TreeConstruction docstring: indent the parameter list
RST tweaks for Bio.Phylo

Makes an example into a literal block, and adds a description to the
target_tree parameter in the get_support which fixes a puzzling RST
warning from epydoc - see issue #425.
Update ReportLab URL in README
BLAST+ 2.2.30 deliberately removed -word_size for RPS-BLAST

According to the BLAST developers (by email), the word size
is specified when the domain database is built, and so the
option should never should have been in rpsblast and rpstblastn.

TODO: Remove this from our rpsblast and rpstblastn wrappers.
Fix import not matching usage; PEP8

Spotted browsing landscape.io coding style report.
Remove unused import
Try to fix use of undefined variable in Bio.Geo; PEP8 whitespace

This probably needs more test coverage...
PhyloXMLIO: choose a default text encoding for XML output on Py2/3

Based on @peterjc's phyloxml_py3 branch.

Should resolve Issue #368 and Issue #334.