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* Add `force_update` to `RepoContext` and propagate it through install/update flows * Add `pkgmgr install --update` to force re-running installers even if the same CLI layer is already loaded * Enhance `NixFlakeInstaller` to ensure correct outputs (pkgmgr + optional default for package-manager) and support refresh/upgrade with index-based fallback remove+reinstall * Make Python/Makefile installers emit an “upgraded” marker when `force_update` is used * Add E2E tests for “three times install” scenarios (makefile, nix, venv) with shared run helper * Fix git safe.directory wildcard quoting in E2E shell runner and minor cleanup/reordering of imports/comments https://chatgpt.com/share/693db0b4-6ea4-800f-b44a-f03939c7fb9e