There are a lot of settings in qmake.conf that qmake needs to know, so it will read it anyway.
"CONFIG += qt" in short means: "link with Qt", but if you take a look at $QTDIR/mkspecs/features/qt.prf, you'll see this isn't that easy to reproduce just by setting some variables in a .pro file.
If that's a common problem, then maybe Trolltech support has some ready made solution for this?
If you don't want that additional Makefile and there are no other ideas, you can also consider using other build systems:
With CMake it should be doable using just one CMakeLists.txt file --- it's just a matter of resetting some variables. I don't know much about the other two build systems, but they're are similar to CMake.





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