Add Nix configuration defaults and new shallow-clone integration test

- Enable 'nix-command' and 'flakes' globally via flake.nix nixConfig
- Improve .gitignore by excluding *.log files
- Add integration test for shallow clone mode using pkgmgr install pipeline
- Ensures pkgmgr works end-to-end inside test container with --clone-mode shallow

See: https://chatgpt.com/share/69332bc4-a128-800f-a69c-fdc24c4cc7fe

.gitignore

@@ -28,3 +28,6 @@ Thumbs.db
 
 # Nix Cache to speed up tests
 .nix/
+
+# Ignore logs
+*.log

flake.nix

@@ -1,6 +1,10 @@
 {
   description = "Nix flake for Kevin's package-manager tool";
 
+    nixConfig = {
+    extra-experimental-features = [ "nix-command" "flakes" ];
+  };
+
   inputs = {
     nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
   };

tests/integration/test_integration_install_pkgmgr_shallow.py

@@ -0,0 +1,46 @@
+"""
+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
+
+
+class TestIntegrationInstallAllShallow(unittest.TestCase):
+    def test_install_all_repositories_shallow(self):
+        """
+        Run: pkgmgr install --all --clone-mode shallow --no-verification
+
+        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",
+                "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
+
+
+if __name__ == "__main__":
+    unittest.main()