JNRPE 2 tries to be as compatible as possible with JNRPE 1.x. However, since the core of JNRPE has been completely rewritten, if you have implemented some custom plugin, you'll have to make some changes.
To make some changes minimal, a 'compatibility library' has been created: simply put that library into your classpath.
Using that library the changes you have to make to your plugin are very simple: you just have to change all the references to CCommandLine to references to ICommandLine.
All the core plugins has been ported to the new version.