I don't think so, in any conventional sense. The provided ability to run QuPath from a command line is currently very limited, but may change and improve in the future.
You should be able to run QuPath from other directories if the paths can be set appropriately, but I don't have any particular method to suggest. You might want to look into how to specify the classpath / Java library path, or setting the current working directory, when running a java application from the command line in general.