Don't store scores and settings in the home directory, on Linux at least. You should follow XDG base directories for that. You should do something like XDG_CONFIG_HOME/sandtrix/settings.properties for settings, and XDG_DATA_HOME/sandtrix/highscores.data for high scores.
If you still want to name directories with the game's version, do something like XDG_CONFIG_HOME/sandtrix/1.4/settings.properties.
For MAC, follow this. And for Windows systems, you should do something like this.