Actually the game is saving into the 'saves' folder of the game folder
You should put this folder into the user folder (~/.factorio/saves or something like that)
Why this modification should be implemented ?
- Your saves is no longer dependent of the game folder, but the linux user folder (for exemple in windows saves files are in user folder/roaming/factorio/saves)
- Factorio will be more "linux compliant" (it is a common habit for linux games/softwares to put their config/save into the user folder, their is lots of good reasons for that)
- Nobody making bad assuming will lose their saves : Ideleted the factorio folder of the last version with my saves in it, assuming it was like most other linux games
In case my suggestion doesn't interest the game developers : no problem, i'll make a symbolic link into the game pointing on my user folder

I'm a linux developper and I really enjoy your game ! (fun; smart and every logical details are very well handled)
Continue your great job !