feat(install): add --update to re-run active-layer installers and improve Nix refresh logic

* 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

scripts/test/test-e2e.sh

@@ -49,7 +49,7 @@ docker run --rm \
       # Gitdir path shown in the "dubious ownership" error
       git config --global --add safe.directory /src/.git || true
       # Ephemeral CI containers: allow all paths as a last resort
-      git config --global --add safe.directory '*' || true
+      git config --global --add safe.directory "*" || true
     fi
 
     # Run the E2E tests inside the Nix development shell