Description

After 60 pull requests, only 1 repository remains un-updated: https://github.com/uclahs-cds/docker-MToolBox/pull/1. That repo doesn't have a working image yet, so I'm not overly concerned with breaking its workflow.

With all that, we're ready to enact Step 3 from #12 and merge refactor_base into main!

Closes #6 Closes #8 Closes #10 Closes #13 Closes #15

Checklist

[x] This PR does NOT contain PHI or germline genetic data. A repo may need to be deleted if such data is uploaded. Disclosing PHI is a major problem.
[x] This PR does NOT contain molecular files, compressed files, output files such as images (e.g. .png, .jpeg), .pdf, .RData, .xlsx, .doc, .ppt, or other non-plain-text files. To automatically exclude such files using a .gitignore file, see here for example.
[x] I have read the code review guidelines and the code review best practice on GitHub check-list.
[x] I have set up or verified the main branch protection rule following the github standards before opening this pull request.
[x] The name of the branch is meaningful and well formatted following the standards, using [AD_username (or 5 letters of AD if AD is too long)]-[brief_description_of_branch].
[x] I have added the major changes included in this pull request to the CHANGELOG.md under the next release version or unreleased, and updated the date.