There's lots of stuff that is modified on this server, I will briefly explain the gist of the changes

My test server, Alec's Otherwise, is running on a Debian Linux server. Instructions for installing gmod dedicated server on linux can be found here:
http://wiki.garrysmod.com/page/Linux_Dedicated_Server_Hosting
There is a saved version of the webpage (saved 1/1/2016) in
wintersurvival2/to-do/notes-resource/Linux Dedicated Server Hosting - Garry's Mod.htm

using the fallowing starting script:
located at /home/steam/server_1/run_server.sh
---------------------------run_server.sh----------------------------------------

#update the server with the code from queue branch
cd garrysmod/gamemodes/wintersurvival2/
sudo git checkout master
sudo git merge queue
cd ../../../

#run the gmod server
./srcds_run -game garrysmod -disableluarefresh +maxplayers 28 +map ws_abandon_night +gamemode wintersurvival2

-----------------------end run_server.sh----------------------------------------

As the script might suggest, gamemodes/wintersurvival2 is a git directory that is symlinked to another user's directory that I use to manage all the git directories.

Additionally, this server will not automatically refresh lua code (doing so breaks the gamemode slightly) so that I can checkout and merge code while the server is running. (this can be reset by remove the -disableluarefresh flag)

as an additional note, I usually run the script from a tmux session, so that I can log in remotely later and still attach to the tmux session