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@ned-deily As I worried, there are flow on effects. Because sys.executable is no longer a real file or a real symlink, some operations break down.
There has to be a trade-off between "can I use sys.executable later to execute Python" vs "can I open(sys.executable) or make a link to sys.executable", and I think the former should win. Hopefully this is narrow enough that it only impacts Store users, and we can give it as another reason you may need to switch to the regular installer.
FWIW, I agree that the main purpose of sys.executable should be to facilitate executing another instance of the current Python so that sounds like the right tradeoff. Also, FWIW, in macOS framework builds, sys.executable points to the so-called stub launcher executable, not to the actual interpreter binary, and the path is often not within sys.prefix. (That's true for Python 3; in Python 2, that behavior was never changed and still causes problems here and there with tests and the like.) So there is some precedent for divergence here.
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https://bugs.python.org/issue37369