To install mods to your ArmA 3 server simply export your active modlist as modlist.html
Then upload the file into your File Manager
Your ArmA 3 server will then automatically download, update and load up all the mods in that list each time it starts up.
Note: This only works with Workshop mods and private mods will need to be uploaded then added to the “Additional Mods” section in the Startup tab
To upload missions, simply drop the mission pbo files into the mpmissions folder in the File Manager
Your game settings will be found in the server.cfg and basic.cfg, both can be found in your File Manager
A much better source of information for configuring this can be found on Bohemia's own wiki here:
As well as config generators here:
This is a simple fix, the default steamProtocolMaxDataSize in server.cfg is too low so it's unable to send the full mod list.
Simply set:
steamProtocolMaxDataSize = 16384;
in server.cfg