Qmlproject files in subdirectories are implicitly included

Qmlproject files in subdirectories are implicitly included into the main qmlproject file and may mess up project parsing.
I simplified a scene from a customer that shows the issue.

In the content folder of the project I added a qmlproject file with a file filter which lets the file App.qml appear 2 times in the project explorer. 
As a side effect this prevents the cmake exporter from working correctly.