basic cmd integration test

The new ./test/cmd/run script runs through a basic set of pydarm subcommands to test basic functionality, including report generation, ls, commit, and export.

Included is a data.zip file which includes all data files needed to run through the test. It will be unpacked automatically by the run script. This is tracked with lfs.

The integration test is the last commit. The previous commits are some minor code cleanup needed to make the self-contained integration test function properly.

Best to review each commit individually.