Revert "feat(flags): script arguments come after '--'" (#3681)

Due to complaints about ergonomics and because it breaks shebang on
linux.

This reverts commit 2d5457df15.

BREAKING CHANGE

std/fs/empty_dir_test.ts

@@ -217,13 +217,12 @@ test(async function emptyDirPermission(): Promise<void> {
       args.push(
         path.join(testdataDir, s.async ? "empty_dir.ts" : "empty_dir_sync.ts")
       );
-      args.push("--");
       args.push("testfolder");
 
       const { stdout } = Deno.run({
         stdout: "piped",
         cwd: testdataDir,
-        args
+        args: args
       });
 
       const output = await Deno.readAll(stdout);