Fixes #996
Merge pull request #997 from jrrideout/issue-996

Fixes #996
added check for qcli
updated to import command line processing functionality from qcli
added qcli to dependency list
updated changelog to mention qcli dependency
removed as we're now using code from qcli
removed make_qiime_rst_file.py in favor of qcli_make_rst
updated changelog
Update add_alpha_to_mapping_file.rst
ported run_script_usage_tests to qcli
ported qiime_system_call to qcli
updated to reflect new parameter names since prot to qcli
ported timeout functionality to qcli
Merge pull request #1007 from casaburi/master

Update add_alpha_to_mapping_file.py documentation
Merge pull request #1006 from gregcaporaso/qcli-port

modifications to qiime to use command line interface framework from qcli

Note, this works fine but not sure about: 
                         qcli version:	0.0.0-dev