Add git stash to avoid possibly breaking builds

* copy more configs into jar
* add hardcoded linux-amd-64 parameter to maven build
	Would be better to use variable and dynamical configuration
	of OS distribution - but then this is easier for now and we know
	on which OS we start this skript.
Merge pull request #521 from lobid/startscript-build-hbz01transformation

Add git stash to avoid possibly breaking builds