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> I don't recall what the issue was the resulted in the check-in that you
> mention.
I think it was http://bugs.python.org/issue8577. The issue was about having srcdir != builddir. The initial patch caused a test failure, and 356d0ea8ea34 fixed (or at least silenced) the failure.
> How was python itself configured (configure command line)?
I tried it with both
 ./configure
 make
and
 mdkir release
 cd release
 ../configure
 make
It fails with both.
> What OS are you running on? Given the shell prompt I'd say Mint Linux. 
Yes (in a VM).
> And finally, is '~/Repos/cpython/python' a checkout or installed 
> location (that is, did you run 'make install')?
It is a checkout.
The argument passed to _safe_realpath() (either "." or ".." in my case) should be interpreted relative to the directory containing the Makefile. But os.path.realpath() assumes that its argument is either absolute or relative to os.getcwd(). It therefore returns the wrong absolute path.