modify qiime to use qcli for command line parsing

[gregcaporaso]

QIIME should import all command line interface and command line interface testing functionality from qcli rather than PyCogent.

• [x] update imports from scripts (this is easy as only util.py needs to be modified)
• [x] update documentation and print_qiime_config to reflect the new qcli dependency
• [x] port script interface testing framework to qcli and update imports in qiime
• [x] port make_qiime_rst_file to qcli and remove from qiime
• [x] port make_qiime_py_file to qcli
• [ ] modify QIIME's make_qiime_py_file to not overlap with what is in qcli - the functionality for generating test files and library files in here is still useful (that's not in qcli, as a lot of the test code generation functionality is QIIME-specific), but functionality for creating scripts should only be in qcli

Work is being done on this in @gregcaporaso's fork of QIIME (branch qcli-port).