I am seeing this:

But the project.clj file is ignored when running lein cljfmt check (empty configuration), unless I specifically specify it (lein cljfmt check project.clj).

I've narrowed it down to (seq paths) never being empty when the paths come from the Leiningen plugin:

Do you want a PR changing lein-cljfmt to always include the project.clj file?

I was thinking that it could look something like (changing lein-cljfmt/src/leiningen/cljfmt.clj):

-           (filter #(and (.exists %) (.isDirectory %)))))))
+           (filter #(and (.exists %) (.isDirectory %)))
+           (concat '("project.clj"))))))

It seems to be a good fit since the project file is lein specific anyway.