Xavier de Gaye <xdeg...@gmail.com> added the comment:

Actually, sys.prefix is '/usr' because '/usr/bin' is in PATH while '/bin' is 
not in PATH. After adding '/bin' to the start of PATH, then sys.prefix becomes 
'/.' when Python is run as 'python3'. The confusion comes from the '/bin' 
symlink (archlinux is not a perfect choice for those tests). Whatever the value 
of PATH, '/bin/python3' has also '/.' as its sys.prefix.

So Modules/getpath.c fails to get '/' as the prefix in step 3 of the algorithm 
described at the top of the source code and uses '/.' (i.e. PREFIX) instead. 
This is caused by its reduce() function not handling the corner case where 
Python is installed on '/'. I will update the PR shortly.

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<https://bugs.python.org/issue31114>
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