STL tags are included elsewhere
Changed stdout output in scripts to stderr;
updated changelog
pep8
ignore Doxyfile
Merge pull request #648 from ged-lab/fix/odds-n-ends

Fix/odds n ends
Fixed for pep8
polished for pylint
Merge pull request #626 from b-wyss/fix/scriptstderr

Changed stdout output in three scripts to stderr
Updated scripts to use add_threading_args from khmer_args
Removed khmer/threading_args.py as it is now depreicated and irrelephant.
Spacing fix
Updated changelog
Chanelog formatting
Resolved some merge conflicts

Conflicts:
	scripts/do-partition.py
	scripts/load-into-counting.py