FreeOrion currently uses the ~/.freeorion directory and puts a lot of stuff in it.
I recommend using the ~/.local/share/freeorion, ~/.cache/freeorion and ~/.config/freeorion directories instead. Many other software already do, like the Transmission bittorrent client, or Wesnoth.
The main advantage is that you follow the same kind of hierarchy as the system on which you are. Also, it reduces the number of “dotfiles” in the user directory and ease navigation.
~/.config/freeorion/ should store the config.xml file.
~/.local/share/freeorion/ should contain at least the saves and the logs.