Code Obfustication or Code Security for a Java/J2EE Web Application

How to Ensure a Secure Build –Code Security more specifically called as Code obfustication—When we deploy a Jaa/J2EE (.war,.ear) web application at Client Site how to make sure of the security of code ,Is there any such standard Security Measures to ensure Code Security and Re-use from a Code Level or is it only that we sign some NDA/Agreement that code is not reusable and is our Intellectual Property.
Any Inputs are appreciable.