I am constantly asked how to remove the data-sources.xml file from a deployment EAR file. The issue here is JDeveloper is automatically configured to bundle a data-sources.xml file during deployment which is basically all your JDeveloper connections created as a entry for each connection. The easy way to avoid the data-sources.xml being bundled during deployment is as follows BUT there is a catch to doing this.
Choose Tools > Preferences to display the Preferences dialog.
Select Deployment on the left side.
Deselect Bundle Default data-sources.xml During Deployment.
The problem is once you deselect the option as shown above if your running an application in the embedded OC4J server and it requires the data-sources.xml then you will get runtime issues. The trick is to switch it on while testing in the embedded OC4J server and then switch it off at deployment time.
This issue is documented here: