Now package the sem folder as a .pbo file ( I am using PBO Manager).
Copy the SEM_config.sqf file and the sem.pbo file over to you server @epochhive/addons/ folder.
Copy over from your server the mpmissions/epoch.<island you are using>.pbo
Unpack it somewhere.
Edit the file init.sqf
Add this to the bottom:
//Simple Epoch Missions
if(hasInterface)then{execVM "semClient.sqf"};
Close and save.
Copy the file MissionFile/semClient.sqf from the SEM download to the root of the epoch.<island you are using> folder.
Save and repack the epoch.<island you are using> folder into a .pbo
Now copy that file to your servers mpmissions/ folder.
You are pretty much done.
Next is to update your battleye filters which can be found here (Just do Step 3):
https://github.com/KiloSwiss/Simple-Epoch-Missions
Remember to copy over your battleye files to your server after editing.
Restart your server and enjoy!
EDIT: Remember that updating the script will break it again! Not sure why scriptDone does not work with execVM on linux but does with spawn compile preprocessFileLineNumbers as the two are functionally identical.