Write pathing jar of run-class.sh into its own directory

Currently, the pathing.jar file used to specify the classpath for run-class.sh is written directly into the top-level working directory of the app. When using container images, there may be some predefined permissions set on the working directory. This may cause permission issues with being able to write the pathing.jar file.

Creating a separate directory for the pathing.jar will make it easier to manage the permissions.