Android Studio: Android Manifest doesn't exists or has incorrect root tag
On Android Studio v0.8.2 clicking on Sync project with Gradle files
button solved my problem.
update
Thanks to the comment of jaumard. If the Sync project with Gradle files
it's not visible you have to open the Gradle panel and click sync icon on top the toolbar.
Just call (in any case) File -> Invalidate Caches and Restart....