I got a second (ungracefull) AndroidManifest.xml file by including an Android.R package instead of the com.example.mypackage.R.
Symptoms: build seemed to work, but launching showed the existing Error in workspace, which needed to be fixed first.
One AndroidManifest.xml was found in classes, the other in a file called resources.ap_ .
I simply quickfixed (include android.R) workspace to hell.
edit: didn't work either, workspace still in in hell; problems in projects, which liked to be fixed...
edit1: can't find the package, with should hold the AndroidManifest.xml.
edit2: I consider to assume the second Manifest File in Android.jar - seems like each Manifest file results in generated 1 R.class. I erased complete workspace. Because it was playground anyway. (Then I set up Git.)