Newer git versions update some cache in .git/index even on read-only calls (like git status). So ignore any changes in .git when checking make clean.
@@ -36,7 +36,7 @@ else
fi
ok=true
-diff "$diff_opts" -r "$clean_dir" "$top_dir" > "$diff" || ok=false
+diff "$diff_opts" -x .git -r "$clean_dir" "$top_dir" > "$diff" || ok=false
if [ "$ok" == true ]; then
echo "Source tree is unchanged. :]"