Spigot 1.13.2 latest
ItemJoin 5.0.3-b209

I skipped b208, in favor of b209. I manually updated the configuration, and it seems fine. Automatic configuration update does not pick up non-default values. :(

I assume that the version 7 config.yml will be clearly documented. I wasn't sure exactly what to do in some cases, so took what looked to be the correct routes.

Yeah, it will be clearly documented.

What do you mean by "Automatic configuration update does not pick up non-default values."?
You are saying that if you change a value in the new config it doesn't register?

Most of the config settings are all in the same spots but properly setup so I can modify them in the future.

Stuff that was renamed; (New Value - Old Value)
Obtain-Items - Items-Permissions
Obtain-Items-OP - OPItems-Permissions
Commands-Get - GetItem-Permissions
Commands-OP - OPCommands-Permissions
Movement-Bypass - InventoryBypass-Permission

DataTags - NewNBT-System

(Everything else should be self-explanatory as their names weren't changed except their root node).

I mean that as a test, I let the plugin convert my version configuration to version 7. T he values I had changed from defaults in version 6 configuration where not transferred to the automatically-updated version 7 configuration.

In my other test, I manually transferred the changes.

Ohhh yeah, the version change doesn't transfer the values from the old config file.
I went back and forth on this deciding if it is the right call and I am still kind of debating it. The thing is it leaves open a few security issues with the old configuration data and I don't want to risk data corruption. -- Which is why since the dawn of creation when changing configuration versions I would always have ItemJoin automatically save the old config files and check for file integrity before generating a new version.

I'm still open to suggestions it just becomes the issue of seeming really redundant.

Once we see full documentation of the version 7 nodes, it should be fine. I had to make a few guesses, but I'll revisit them when the documentation is posted.

ItemJoin v5.0.3 has officially been released.
You can grab it here; https://www.spigotmc.org/resources/itemjoin.12661/download?version=262715

Please read the changelog as the documentation has not been updated yet;
https://www.spigotmc.org/wiki/recent-changes

You will now see that the changes have been reflected here; https://www.spigotmc.org/wiki/configurations/

If you have any more questions regarding this please re-open this issue.

Thanks. All good.