Update MANIFEST to include Doc/examples/my_blat.psi

Identified by Lin (林行众) on the mailing list - thanks!
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010601.html
Fix testing with clustalw 1.83

Old test worked with clustalw 2.1 but the behaviour of 1.83 was
slightly different leading to the unit test wrongly failing:
http://lists.open-bio.org/pipermail/biopython-dev/2013-May/010599.html
Skip test_bgzf.py if Python's gzip is broken
Skip Bio.bgzf doctest if gzip broken http://bugs.python.org/issue17666
Can't import anything from Bio in run_tests.py
Revert moving import (must be after edit PYTHONPATH)
Stupid typo, broken under Python 3
Skip BGZF tests in test_SeqIO_index.py if issue 17666
Updated FastaWriter documentation to reflect reality

Someone must have edited the code and didn't update the documentation for FastaWriter.
Added color_scheme keyword to weblogo to allow users to set their own colors (suggested by Anthony Mathelier of UBC)