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

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";
   };