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Related to https://github.com/astral-sh/uv/issues/15113 The case in the linked issue is that we perhaps should not be allowing `uv run --with` with system interpreters at all. I think we can consider that, but the issue highlighted that `uv run --with` for a system interpreter is broken if the base interpreter has custom site packages. This generalizes beyond system interpreters so we should probably fix our overlays.