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

@@ -27,4 +27,7 @@ build/
 Thumbs.db
 
 # Nix Cache to speed up tests
-.nix/
+.nix/
+
+# Ignore logs
+*.log