Update code and fix bugs

[RlyehAD]

1. The code has been updated to be consistent with the latest versions of mmelemental, cmselemental and mmic. This update provides a foundation for the packages using mmic_cmd to run smoothly.
2. The CI tests can be passed. But there's still problems with the doc action.

TO DO

1. Make the repo pass the doc processes.

[lgtm-com]

This pull request fixes 1 alert when merging 4012d33 into 9039018 - view on LGTM.com

fixed alerts:

• 1 for Wrong name for an argument in a call

[anabiman]

I would like to retain outfiles_track to make this applicable to processing large data files. For now, this component works only with a fork of QCEngine. Maybe the best way to get around this is by replicating the util.execute functionality from QCEngine in this component.

[anabiman]

I have moved some of the needed functionality from QCEngine to this pkg. The cmd component now works. Please update your PR accordingly @RlyehAD.