Enabling Mods on a Dedicated Server
As of the recent Alpha 0.9.9.0 release the way mods were previously activated has been changed. This guide assumes that you have a working Barotrauma dedicated server, with access either via RDP/FTP and some kind of text file editor.
Procedure
One of the easiest ways to have you client and dedicated server running the same set of mods is to first enable the mods you wish to use in your client (your pc). This method is simple and does not rely on steamcmd mod subscription.
Enabling Mods on Client
Firstly go the the steam workshop and subscribe to the mods you wish to use. Make sure that steam has finished downloading the mods before relaunching Barotrauma.
From the main menu select settings -> Under the content packages, enable each of the mods you would like to use on your server, some mods may require a game restart, do this now.
The Mods folder (where the mods are stored) is located in the root game directory (Barotrauma\Mods), this will reside in the steamapps folder -> common, if you're unsure where you installed Barotrauma, right click the game on steam -> properties -> local files tab -> then click on browse local game files, which will drop you in the games root directory.
You will need to copy the mods you wish to have activated to your dedicated server Barotrauma\Mods directory, via RDP,FTP,SMB,locally etc, depending on your server setup.
Enabling the Mods on the Server
Now that the mod files have been copied to the server, navigate to Barotraumas root game directory on the client (which you found before). Open the file config_player.xml with your favorite text editor (Notepad/NP++/Sublime).
Scroll until you find the line <contentpackage
path="Data/ContentPackages/Vanilla 0.9.xml" />
You should see multiple <contentpackage/> entries each representing mods that are currently enabled. On the server, in the games root directory, open the config_player.xml and compare these entries, only the vanilla package should be enabled on your unmodded server.
Copy these entries into the config_player.xml on the server - this will enable the modifications for next launch.
Run the server with the executable (windows) or shell script (nix).