All the apps in our builds get the status of "built-in" as opposed to "downloaded". This makes them impossible to uninstall.
If we want to debug one of our apps with DS-5 CE, we must allow it to be uploaded and installed by DS-5. That's how this tool works.
You can't install the same app twice and you can't delete a built-in app. So we need to remove the app to be debugged from the build which is inconvenient.
You may have to mount /system/app writeable (which I think is OK for a developer edition like Linaro Android, it could be a build option?) and muck around in the database yourself since neither adb uninstall or the Settings app is keen on removing a built-in app. Can it be done?