src/Pure/Admin/component_jedit.scala

       for {
         file <- File.find_files(Path.explode("~~/src/Tools/jEdit/patches").file).sortBy(_.getName)
         name = file.getName
         if !File.is_backup(name)
       } {
-        progress.bash("patch -p2 < " + File.bash_path(File.path(file)),
-          cwd = source_dir, echo = progress.verbose).check
+        val patch = File.read(File.path(file))
+        Isabelle_System.apply_patch(source_dir, patch, strip = 2, progress = progress)
       }
 
       progress.echo("Augmenting icons ...")
 
       val jedit_icons_path = source_dir + Path.explode("org/gjt/sp/jedit/icons/themes")