One simple way is to package your code in a jar. Be sure to include a main in one of the class that starts your crawling. Drop that jar file in the lib folder of your Nutch installation. You can now start your crawling with a command like (assuming that your PATH is correctly set to find the nutch command):
nutch com.xyz.YourCrawlerMain
where "com.xyz.YourCrawlerMain" represents your main class to launch your crawling.
This will launch your crawler with the Nutch classpath correctly set.
For the configuration files, just update them directly in the conf folder of your Nutch installation.
UPDATE
I'm working on something similar and I am able to make nutch work from my app with these settings: set your classpath to include the Nutch folder (so it can find the plugins), the Nutch/conf folder and include all jars from Nutch/lib + nutch.jar from the nutch folder.
But beware if your app is running in a web container. I had to mess with the classpath to make it works...