Add output handler to print list of strings

Necessary for print_biom_python_config.py.

Also fix optparse code to allow for commands that have no required options.
Merge pull request #146 from jrrideout/death-march

Add output handler to print list of strings
Fix #147
Merge pull request #148 from jrrideout/death-march

Fix #147
Add a couple more input handlers.

Necessary for subset_biom.py conversion. Also fix file writer handler to work better with generators (also necessary for this conversion).
Merge pull request #152 from jrrideout/death-march

Add a couple more input handlers.
Merge pull request #156 from wasade/death-march

allow pyqi driver to use commands in current working directory
Remove pyqi driver config file
Added old_to_new_command

Credit goes to @gregcaporaso for writing this.
Merge pull request #158 from jrrideout/death-march

Remove pyqi driver config file
addressing conflicts
addresses #154