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How you deploy your EAR depends on the type of environment you have. For "OnSite" deployment you would need to contact the production system administrator to have your application deployed on the production WLS. The administrator would decide where and how the application is deployed, the process would be specific to the site.
The security behavior depends on the configuration, e.g. when you enable security on your application various [url http://docs.oracle.com/cd/E14571_01/web.1111/b31974/adding_security.htm#BGBDEHFH]files are created / updated. When deployed to production these configurations need to be changed to suite the production instance, i.e. in development environments authentication is enforced by security constraints while in production this is achieved e.g. using OAM policies. The specific details depend on the instance.
For Cloud environments you would need to deploy the application e.g. on [url https://cloud.oracle.com/mycloud/f?p=service:home:0]Java Cloud Service instance as applications cannot be deployed on the Cloud production instance.
To integrate with the navigator menu refer to the [url http://docs.oracle.com/cd/E15586_01/fusionapps.1111/e16691/ext_nm.htm]Customizing the Navigator Menu documentation.
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