dude

src/babashka/main.clj

@@ -722,9 +722,10 @@ Use bb run --help to show this help output.
   (let [opt (first options)]
     (if (and opt (and (fs/exists? opt)
                       (not (fs/directory? opt))))
-      [(next options) (assoc opts-map
-                             (if (str/ends-with? opt ".jar")
-                               :jar :file) opt)]
+      [nil (assoc opts-map
+                  (if (str/ends-with? opt ".jar")
+                    :jar :file) opt
+                  :command-line-args (next options))]
       [options opts-map])))
 
 (defn parse-opts
@@ -1152,6 +1153,7 @@ Use bb run --help to show this help output.
                     (:jar opts))
           (parse-file-opt args opts)
           [args opts])
+        ;; _ (prn :args args :opts opts)
         abs-path #(-> % io/file .getAbsolutePath)
         config (cond
                  config (if (fs/exists? config) (abs-path config)

test-resources/script_with_overlapping_opts.clj

@@ -0,0 +1 @@
+(prn (first *command-line-args*))

test/babashka/main_test.clj

@@ -1,6 +1,7 @@
 (ns babashka.main-test
   {:clj-kondo/config '{:linters {:unresolved-symbol {:exclude [working?]}}}}
   (:require
+   [babashka.fs :as fs]
    [babashka.main :as main]
    [babashka.test-utils :as test-utils]
    [clojure.edn :as edn]
@@ -71,7 +72,8 @@
            (-> (let [[_ opts] (main/parse-file-opt ["-e" "(prn :foo)"] {})]
                  (main/parse-opts ["-e" "(prn :foo)"] opts)))))
     (is (= {:file "foo", :command-line-args ["README.md"]}
-           (main/parse-opts ["README.md"] {:file "foo"})))))
+           (main/parse-opts ["README.md"] {:file "foo"})))
+    (prn (bb nil (fs/file "test-resources" "script_with_overlapping_opts.clj") "--version"))))
 
 (deftest version-test
   (is (= [1 0 0] (main/parse-version "1.0.0-SNAPSHOT")))