slapos node prune already detected the case where software was running
and refused to run while software was runnning, to prevent a case where
software writes files and prune removes them because they are not yet
referenced, but nothing prevented the other way around: slapos node
software should not start while slapos node prune is deleting files. To
prevent this, make slapos node prune actually use software pid file,
then software will refuse to start while prune is running.