qmake generates corrupt Xcode projects with duplicate references

Getting warnings that should be documented from Qt Creator managed projects.

There are other issues with iOS Simulator, but this is a documentation entry for Qt Creator 3.4.1 for Qt 5.4.2 on macOS 10.10.2 on Xcode 6.2

/Applications/Xcode.app/Contents/Developer/usr/bin/make -f Makefile.ReleaseSimulator
2015-08-17 11:37:04.145 xcodebuild[1915:53948] warning: The file reference for "/macdev/qdevtest/testqml/Rpzqml.qrc" is a member of multiple groups ("Supporting Files" and "Resources"); this indicates a malformed project. Only the membership in one of the groups will be preserved (but membership in targets will be unaffected). If you want a reference to the same file in more than one group, please add another reference to the same path.
Build settings from command line:
SDKROOT = iphonesimulator8.2