Fixed get_place_output_all_jplace to look for placement files in the treeDir instead of blastDir
Allows continuation of placements if a marker package does not exist
Merge pull request #395 from gjospin/20121204_missing_Codon_markerfix

Allows continuation of placements if a marker package does not exist
Fixing broken individual steps issue. Closes #405
Update phylosift.tex
Merge branch 'devel'

Conflicts:
	lib/Phylosift/Command/all.pm
	lib/Phylosift/pplacer.pm
	writing/phylosift.tex
Merge branch 'master' into devel
version bump in preparation for release