modifications to qiime to use command line interface framework from qcli

See the [qcli](https://github.com/bipy/qcli) project. 

This pull request contains all of the necessary changes in QIIME to use ``parse_command_line_parameters`` and ``make_option`` from ``qcli`` rather than PyCogent (or more recently ``qiime/pycogent_backports``). 

Before this gets merged, we'll need ``qcli`` to be including in the jenkins runs. 

So far, this code is more or less a direct port from ``pycogent_backports`` so I'm comfortable with it being merged now (and the sooner it is, the better, for testing purposes). However, this will require everyone using dev version of QIIME to install ``qcli`` (which is easy). There are several outstanding issues that I will be continuing to work on, either in the this pull request, or in ``qcli``. These are covered in QIIME's [#1005](https://github.com/qiime/qiime/issues/1005) and in the [qcli issue tracker](https://github.com/bipy/qcli).

I think we'll need @jrrideout involved to merge this PR, as he's our current Jenkins master, but he's out for the next couple of weeks. @jrrideout, let me know if you want to merge this soon, or wait until you're back in the office (and if I don't hear from you, I'll assume the latter). We need to give all dev users a heads-up before we merge it.