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Go to your panel. 
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Click “File Manager” or use SFTP. 
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Drop mods in the appropriate folder: 
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mods/for Minecraft, ARK, 7DTD, Factorio
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plugins/for Paper/Spigot servers
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addons/for Garry’s Mod
Restart your server after uploading.
(Note: For Minecraft Java Servers, their is a built in plugin and version installer and works more seamlessly)

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