Ken, thanks so much for sharing your expertise. I do run CentOS Linux. As you may have surmised I have recently taken over Moodle admin at a school some months ago and and am still learning (every day). I inherited a pretty well set-up situation so it's a good place to learn and see how to build without starting from scratch.
The codebase is managed through a Git repo and all the "extra" plugins are submodules. So to deploy my codebase, in theory, I just clone the repo and pass -recurse--submodules with the command. In practice, I have struggled a bit with submodules and have had to do some finagling on individual submodules to get them initialized and pointing to the intended commit, but am getting more comfortable with them now.
In any case, I was able to get my new DEV instance up and running with no issues. I just use the administration->plugins->plugins overview screen to check for updates and new versions.