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[Backport release-25.11] treewide: use overlays to pass a custom stdenv to buildPythonPackage / bulidPythonApplication #477273

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test/overriding: remove python deprecated stdenv override tests

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[Backport release-25.11] treewide: use overlays to pass a custom stdenv to buildPythonPackage / bulidPythonApplication #477273

test/overriding: remove python deprecated stdenv override tests
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