Merge pull request #46 from wasade/death-march

Death march
fixed missing class definition
Merge pull request #59 from gregcaporaso/death-march

fixed missing class definition
Merge pull request #60 from wasade/death-march

Death march
moved files around, partially addresses #55
added still-non-working version of open reference otu picking workflow
fixes #55
updated default logger as it was printing information that we don't need to stderr on every command call
Merge pull request #62 from gregcaporaso/death-march

reorganization of files
Merge branch 'death-march' of github.com:bipy/qcli into death-march