Refactor pkgmgr self-install handling, add pip-enabled Python env to flake, and fix Nix/pip integration

- Rename requirements.txt to _requirements.txt to avoid unintended self-install via PythonInstaller.
- Update flake.nix to provide Python with pip in both devShell and runtime closure.
- Generate a wrapper for pkgmgr that uses the pip-enabled interpreter.
- Adjust NixFlakeInstaller to correctly handle old profile removal and install outputs.
- Update run_command to support string commands and allow_failure.
- Improve integration test by adding nix profile cleanup and debugging output.

Reference: https://chatgpt.com/share/69345df2-a960-800f-8395-92a7c3a6629f

tests/integration/test_integration_install_pkgmgr_shallow.py

@@ -1,43 +1,71 @@
-"""
-Integration test: install all configured repositories using
---clone-mode shallow (HTTPS shallow clone) and --no-verification.
-
-This test is intended to be run inside the Docker container where:
-  - network access is available,
-  - the config/config.yaml is present,
-  - and it is safe to perform real git operations.
-
-It passes if the command completes without raising an exception.
-"""
-
 import runpy
 import sys
 import unittest
+import subprocess
 
 
-class TestIntegrationInstallAllShallow(unittest.TestCase):
-    def test_install_pkgmgr_self_install(self):
-        """
-        Run: pkgmgr install --all --clone-mode shallow --no-verification
+def nix_profile_list_debug(label: str) -> None:
+    """
+    Print `nix profile list` for debugging inside the test container.
+    Never fails the test.
+    """
+    print(f"\n--- NIX PROFILE LIST ({label}) ---")
+    proc = subprocess.run(
+        ["nix", "profile", "list"],
+        capture_output=True,
+        text=True,
+        check=False,
+    )
+    stdout = proc.stdout.strip()
+    stderr = proc.stderr.strip()
+
+    if stdout:
+        print(stdout)
+    if stderr:
+        print("stderr:", stderr)
+    print("--- END ---\n")
+
+
+def remove_pkgmgr_from_nix_profile() -> None:
+    """
+    Best-effort cleanup before running the integration test.
+
+    We *do not* try to parse profile indices here, because modern `nix profile list`
+    prints a descriptive format without an index column inside the container.
+
+    Instead, we directly try to remove possible names:
+      - 'pkgmgr'      (the actual name shown in `nix profile list`)
+      - 'package-manager' (the name mentioned in Nix's own error hints)
+    """
+    for spec in ("pkgmgr", "package-manager"):
+        subprocess.run(
+            ["nix", "profile", "remove", spec],
+            check=False,  # never fail on cleanup
+        )
+
+
+class TestIntegrationInstalPKGMGRShallow(unittest.TestCase):
+    def test_install_pkgmgr_self_install(self) -> None:
+        # Debug before cleanup
+        nix_profile_list_debug("BEFORE CLEANUP")
+
+        # Cleanup: aggressively try to drop any pkgmgr/profile entries
+        remove_pkgmgr_from_nix_profile()
+
+        # Debug after cleanup
+        nix_profile_list_debug("AFTER CLEANUP")
 
-        This will perform real installations/clones inside the container.
-        The test succeeds if no exception is raised.
-        """
         original_argv = sys.argv
         try:
             sys.argv = [
-                "pkgmgr",
+                "python",
                 "install",
                 "pkgmgr",
                 "--clone-mode",
                 "shallow",
                 "--no-verification",
             ]
-
-            # Execute main.py as if it was called from CLI.
-            # This will run the full install pipeline inside the container.
             runpy.run_module("main", run_name="__main__")
-
         finally:
             sys.argv = original_argv