If you have a A/deps.edn with
{:paths ["src/main/clojure"]
:deps {something/else {:local/root "/Wherever"}
}
Then in /Wherever/deps.edn:
{:deps {...}} ;; no paths, just deps.
When you run clj -Spath within A, the dependency will accidentally pick up :paths from the A: /Wherever/src/main/clojure
whereas when you run clj -Spath from within the dependency, it will pick up paths from the system default deps.edn
*Workaround*
Always specify :paths