copied directly from QIIME
rename scripts to reflect move to qcli

the rational for naming of these scripts is that we'll eventually move qcli to a sub-command framework (like git) where there is one main command (qcli) and you pass arguments to it to execute different sub-commands. so eventually i see creating a new qcli script with something like the following:

qcli make_script <some arguments>

so, naming the scripts this way will allow the description of the interface change to essentially be "drop the first underscore from the command".
updated code to reflect port to qcli
updated code to reflect inclusion in qcli
added scripts
copied directly from qiime
fixed error in directory name
renamed to reflect new script name
removed files that can no longer be created
added output file
updated the usage example to not reference QIIME
fixed bad variable name
update option name and description - misunderstood how it was used previously
fixed annoying functionality where output directory needed to exist already
fixed annoying feature where the input directory had to be in /Users/caporaso/code/qcli/qcli_test_data/qcli_make_rst/scripts/:/Users/caporaso/code/qcli/scripts/:/Users/caporaso/code/qcli/qcli_test_data/qcli_make_rst/:/Users/caporaso/code/pprospector/:/Library/Python/2.6/site-packages/:/Users/caporaso/code/rtax-0.98/:/Users/caporaso/lib
added interface test files
Merge pull request #4 from gregcaporaso/master

ported useful scripts from QIIME