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How the problem was fixed (magic algorithm):

i installed the command line tools of xcode (seemingly not included under osx 10.9)

started to compile sage-6.4 from source

stopped the compilation after around 1h and deleted the whole sage-6.4 folder

After that, sage-6.3.app recovered its usual %cython behavior in the notebook.

Could be that only the first step was useful, but no way checking it now.