Stopping
Typically this is not something you'll need to do. Box Of Stops is fine with you just unplugging the Raspberry Pi when you're not using it.
If you do need to deliberately stop Box Of Stops, the following command will do the job in one step:
sudo pkill -ef boxofstops
This will leave Box Of Stops stopped until you either restart it manually, or you restart the Raspberry Pi. By default Box Of Stops will automatically start again when you boot up the Pi, though this can be disabled.
Note, there are separate instructions if you're running under Windows.
Which processes to stop
The pkill command above will simply stop any running processes that contain "boxofstops" in the command line.
If you have other commands running in that directory, you may want to be more selective.
To list the matching running processes:
ps -ef | grep boxofstops
Then look for the process id for the java process in the list and stop this:
sudo kill <pid>
This will also cause the child python process to stop cleanly.