src/Pure/Tools/check_source.scala

   {
     Output.writeln("Checking " + root + " ...")
     Isabelle_System.hg("--repository " + File.shell_path(root) + " root").check_error
     for {
       file <- Isabelle_System.hg("manifest", root).check_error.out_lines
-      if file.endsWith(".thy") || file.endsWith(".ML")
+      if file.endsWith(".thy") || file.endsWith(".ML") || file.endsWith("/ROOT")
     } check_file(root + Path.explode(file))
   }
 
 
   /* command line entry point */