The user can specify which encryption plugin to use by default in the copernicus.ini file, a sample which is below:
[MAIN_SETTINGS] ... CryptographicPlugin=com.tanksoftware.juk.NOCPlugin ...
com.tanksoftware.juk.NOCPlugin is the class name of the plugin, and that class MUST be in the users class path (ie. contained in the copernicus.jar file or in the users jre/lib/ext/ directory.).
The plugin specified in the settings ini is used every time encryption occurs. When files are loaded and decrypted however, the plugin used to encrypt them (if available) will be used instead. There is no supported way to change this behaviour. People upgrading plugins or changing to a different one benefit from this as they just have to set that option, then load and save all of their files.
The NOCPlugin is the shipped with Copernicus and is the default.