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Refactored the E2E update-all test to execute real CLI commands instead of invoking *main.py*. The test is now split into two independent cases: one running *pkgmgr update* directly and one running the same command via *nix run .#pkgmgr*. This improves realism, diagnostics, and parity with actual user workflows inside the container. https://chatgpt.com/share/693c52cb-cc10-800f-994b-5b2940dcf948