Added parameter lookup convenience function.

Still need to update the rest of the config files to use this.
Update config files and fix bug in new function.
Add missing import to make_command

Fixes #128
Update unit tests
added new general purpose output handler
added trailing newline
Merge pull request #135 from gregcaporaso/death-march

added write_list_of_strings optparse output_handler
Merge branch 'death-march' of github.com:bipy/pyqi into death-march
Remove TODO for optparse validation.

Turns out this wasn't needed. Fixes #136.
__all__ uses os.path.join.

Fixes #134.
Add hooks for config validation.

Hooks for validating usage examples, inputs, and outputs when validation needs to have entire list available.
Add option inputs validation

Now ensures that input options don't map to the same Parameter.
Update test comments to refer to correct filename
Add unit test for inputs validation
ParameterCollection ensures unique Parameter names.

Fixes #121.
Add more option info to make_optparse

Fixes #129.
Merge pull request #132 from jrrideout/death-march

Fixes #114 and #128
Factor command listing code out of __all__
Add unit tests for module loading.

Also add docstrings to new functions.
Merge pull request #141 from jrrideout/death-march

Fixes #137