Hello, so the plugin basically does not appear in the permission manager and the text commands don't work. I've tried reinstalling the plugin. I've tried re-updating my server and Oxide. I've tried reloading all my plugins in-game and still nothing. Any help would be appreciated.

Check your oxide/logs for errors.

It says in the log
17:42 [Error] Error while compiling: GatherManager.cs(521,35): error CS0246: The type or namespace name `PlantEntity' could not be found. Are you missing an assembly reference?
17:42 [Error] Error while compiling: ZLevelsRemastered.cs(625,21): error CS0246: The type or namespace name `PlantEntity' could not be found. Are you missing an assembly reference?

would these have something to do with the gardening update?

You are using old versions of those plugins. Those changes were made about half a month ago with a Rust update.

I just downloaded the most recent version earlier and im still getting said errors

You are not updated and using the latest versions from this site if you see those errors.

ok, I just had to completely uninstall and delete whatever version was installed. Everything is working now.