My use case is for calling Cython at runtime. For example, using
cython.inline or %%cython or the SageMath-specific cython() function. In
that case, absolute paths make the most sense since you want to support
the user running Cython somewhere and then doing chdir().
Perhaps we could keep the default of relativizing the paths but support
a parameter like
cython --embed-position=abspath
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