Studio 5 Multiple invocations of object files

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Using the "managed" build option I can not get the project to link. The generated makefile has every object files listed numerous times (20 to 30 times ) and the link results in a massive list of "duplicate" symbols. I can only get it to build if I handcraft a makefile and build with the "External makefile" option. This gives me other problems of course.

I have been trying to find the root of this problem for weeks! Does anyone else see this ?

What do the ATMEL folks say about this -- Studio 5 is now out of beta and such problems should be a thing of the past.