I have two product flavors, free and pro.
The launcher activity for both is different.
But Android studio expects the launcher activity to be in AndroidManifest.xml under src/main/.
Gradle is building both flavors correctly but IDE is not able to pick the correct AndroidManifest.xml from respective product flavors like src/free or src/pro.
This is happening even after choosing the correct build variant as FreeDebug or ProDebug.
I have worked around this by manually changing the run configuration (Run->Edit Configurations... Under the Activity - Launch option), though that's definitely not an optimal solution.