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Adding steam workshop mods to your Starbound server is very easy. There are two ways you can get a file for a mod:
If you download the file from the Starbound forums, save that somewhere you know you will be able to find it easily. It will be saved as a .zip file, unpack it with a zip file archiver and keep the unzipped file for later.
If you download your Mod via Steam Workshop, open the workshop page, and navigate to Steam/steamapps/workshop/content/211820. Within, Steam will save your workshop file. It will save the name of the file as the steam ID associated with the workshop mod. You can find the ID at the end of the URL of the Steam Workshop page it. Copy the mod's folder and move somewhere easy to reference, like your Desktop.
Now that you've finished that, open your GameServerKings Server Management Panel, and log in with the TCAdmin information provided to you within your verification email. From there, go to "Game Services" located in the left hand navbar menu. Now select the "File Manager" button.
Once you're in the "File Manager", find the mods folder. Click on your mods folder to open it, and select the "new file" button. Give your file the same name as your Mod.
Now open your new file and press the "Upload" button. Find your Mod folder containing your Mod's files, then click on the .pak file and upload that.
Once your file is uploaded, go back to your "Game Services" tab and reboot the server. Your mod should now be installed!