Espionage 2 has background processes, the iSpy and the Espionage Helper. For these to run, those processes have to be defined at the system level.
So Espionage 2 has to be properly uninstalled to get rid of those processes.The simplest way is to use uninstall option from the Espionage menu. Trashing the application is not sufficient.
So before moving to Espionage 3 you should uninstall Espionage 2, this will also restore the folders back to normal.
Espionage 3 is simpler, it has no background processes and quit and trash the application will stop all the processes related to it.
Rgds
Zsolt