Using Clojure CLI tools aliases with Cider jack-in has an issue when using -M flag for including aliases, specifically when they are defined in a .dir-locals.el . When cider composes the command line arguments, they are not placed in the correct order (aliases are placed before clj-opts). The -A flag does not have a problem (although that flag is deprecated). https://github.com/clojure-emacs/cider/issues/2916