Its a pixelart rougelike that i found somewhere in my linux package list, tried out, and liked. I could tell you about some mechanics, but its probably better to see for yourself at its website http://shatteredpixel.com/shatteredpd/ or the pixeldungeon community [email protected] .
You can just not git add the one file on the secondary drive when it is not connected. This schould not be that much overhead and (at least for me) it is much simpler than any other solution. Ps: Why do you want that one config file on the external drive and not on the main one?