We have support for unzipping file directly in the file manager view. You can use drag and drop in the file manager, or an actual FTP program to move the file.
Then upload that zip file to the server, to the folder /mods.
This will make a single file that is often smaller then all the separate folders were (and smaller means faster upload). We highly recommend using a program to package and compress the folders, such as a program that does. Upload all the numbered folders for the mods you want to use to the server. Leave the mods in those numbered folders. Inside each folder is a file called contents.pak. The names of the folders are the Steam workshop ID for that mod. Inside there, you will see a folder for every mod that you subscribed to. The ID number for Starbound is 211820, so click on that folder. Those are the master ID numbers of Steam games.
The "mods" folder is where you manually add your own mods, and after a fresh install this folder is usually empty. That is NOT where Steam stores the workshop mods that it downloads automatically. In the screenshot below, you will also see a "mods" folder. To get to where Steam hides the mods, click on the arrow in the upper left to move up one level, which is circled in the screenshot. You will see this view of the game files on your local computer, as shown below. On the next pop-up window, click on the "Local Files" tab across the top, and then on "Browse Local Files".
Preparing the Mods to Upload to the Server For a large number of mods, you might have to wait a little while for Steam to finish downloading them all. When it's subscribed to, the button changes to say "Subscribed" with a checkmark, and Steam has begun to automatically download the mods in the background to the local computer files. Navigate to the workshop for Starbound on Steam, find the mods you're interested in, and click on them to open up their workshop page. The easiest way to get Steam Workshop mods is described below, and starts with subscribing to the mods in Steam Workshop and letting Steam download them automatically to the client on your local computer. Non-workshop mods are installed the exact same way on the server as on your computer simply use the File Manager on the left side of your NodePanel to access the server's mods folder.