it breaks when I add FileOpener. .... It adds some config to the AndroidManifest, but I don't see why it is conflicting, it is not targeting the application tag itself:
...
<config-file target="AndroidManifest.xml" parent="/*">
<uses-permission android:name="android.permission.READ_EXTERNAL_STORAGE" />
</config-file>
But it is. Android manifest root element is <manifest> and only mandatory child is <application> tag.
edit: Another option is that the parent="application" reference triggers this warning.