added run_script_usage_tests
ported run_script_usage_tests directly from QIIME
updated to reflect port from qiime
ported qiime_system_call to qcli
updated for port from qiime
added missing space
added import for convenience
ported timeout functionality to qcli
added missing module
added terminal line break
Merge pull request #5 from gregcaporaso/port-cli-testing

Port cli testing