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/home/sakai/opt - Directory containing programs used in operation of the scripts(eg, groovy/java )
/home/sakai/apps - Directory contaiing various apps(Each script/runnable entity should be considered an app)
/home/sakai/common_lib - Common jars/libs for apps that may be used in the apps. apps don't have to use them, but it should be encouraged to save space.
Each app would be best to have a run.sh like script to run the script easily out of cron, but this is not a requirement.