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Jalien/run.sh fixes

Adrian Sevcenco requested to merge asevcenc/jalien:jalien_fixes into master

run.sh :
exec java (in place) instead of starting a new shell
any jar file in command line will be converted to -cp jar_file:jar_file_directory in java command
jalien :
check for user certificates always (and remove their group/others permissions)
setup arg : keep the existing (possible user customized) configuration files
add cleanup arg : kill lingering java jbox processes - they can keep running even after logout
add run arg : will run any function declared in command line e.g. : jalien run alien.JBox
JALIEN_OPTS : environment set additional java options any other options declared in command line will be prepended to the options list defined by argument options

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