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

tests/e2e/test_install_pkgmgr_three_times_venv.py

@@ -0,0 +1,34 @@
+from tests.e2e._util import run
+import tempfile
+import unittest
+from pathlib import Path
+import os
+
+
+class TestPkgmgrInstallThreeTimesVenv(unittest.TestCase):
+    def test_three_times_install_venv(self):
+        with tempfile.TemporaryDirectory(prefix="pkgmgr-venv-") as tmp:
+            home = Path(tmp)
+            bin_dir = home / ".local" / "bin"
+            bin_dir.mkdir(parents=True)
+
+            env = os.environ.copy()
+            env["HOME"] = tmp
+
+            # pkgmgr kommt aus dem Projekt-venv
+            env["PATH"] = (
+                f"{Path.cwd() / '.venv' / 'bin'}:"
+                f"{bin_dir}:"
+                + os.environ.get("PATH", "")
+            )
+
+            # nix explizit deaktivieren → Python/Venv-Pfad
+            env["PKGMGR_DISABLE_NIX_FLAKE_INSTALLER"] = "1"
+
+            for i in range(1, 4):
+                print(f"\n=== RUN {i}/3 ===")
+                run(
+                    "pkgmgr install pkgmgr --update --clone-mode shallow --no-verification",
+                    env=env,
+                    shell=True,
+                )