Quick Installation Guide
The file you'll download on spigot is not the actual plugin jar, it's a zip file which contains the two different versions of the plugin as well as a few extra unnecessary addons.
Once you download the file from Spigot, open the zip file:
If you're running a 1.13 server, you have to keep the jar called MMOItems 1.13.jar. If you are running an older version (1.8-1.12), you must use MMOItems Legacy.jar. Keep in mind you must only use one jar at a time. You will get (not severe) console warnings if you are using the wrong file, or potentially console errors if you are using both.
The two other files are addons. If you are new to MMOItems, you might not need them right away.
MMOItems WorldDrops allows you to have per-world drop tables for blocks, monsters & mythic mobs. This allows monsters/blocks/mythic mobs to drop different items depending on the world they are killed/mined in. If you want to use this addon, simply drag & drop it in your plugins folder just like you did with MMOItems.
A /drops folder should appear in the /MMOItems plugin folder after rebooting your server. In that folder, each .yml file corresponds to a world drop tables. In order to know how to configurate these YAML config files, please refer to this wiki page.
MMOItems UltraItemUpdater allows you to always keep all your items up to date each time you edit them using the item edition menu. The item updater is a system which allows you to keep every item in player inventories up to date with the most recent changes applied to them in the edition menu, which is very handy if you need to nerf them for intance.
By typing /updateallitems, you can actually enable the item updater for every item you created. This addon will take extra performance, therefore you need to be careful when using it. The item updater was designed to nerf specific items once at a time, and not to keep all items updated - check your timings after running that command during a server players peak, if they seem fine, you may consider keeping this option on.