src/Pure/Tools/update_then.scala

       if (specs.isEmpty) getopts.usage()
 
       for {
         spec <- specs
         file <- File.find_files(Path.explode(spec).file, file => file.getName.endsWith(".thy"))
-      } update_then(Path.explode(File.standard_path(file)))
+      } update_then(File.path(file))
     })
 }