You can edit a deployment descriptor file manually. However, it is preferable to edit a deployment descriptor using a deployment descriptor editor. The deployment descriptor editor is designed to ensure that the deployment descriptor maintains a valid structure and that its references contain appropriate values.
In EJB 3.1, one rationale behind using a deployment descriptor is to override the values that are specified in the Java™ source by annotations. This ability is useful after you have finished developing your EJB application. Now just before you move your application into production, you can specify some final overriding values.
By default, deployment descriptors are created for web projects only; for information about how to change this default, see Selecting default project structures. For information about adding a deployment descriptor to an existing project that does not contain one, see Generating deployment descriptors.
You can use the EJB deployment descriptor editor to address any modifications you want to make:

If you are using EJB 3.1, enterprise archive (EAR) files do not require an application.xml file. When there is no application.xml file, the product examines the Java archive (JAR) file contents to determine whether the JAR file is an enterprise bean (EJB) module or an application client module. If the JAR file contains more than one type of deployment descriptor, remove the extraneous deployment descriptor.