src/Pure/PIDE/headless.scala

           }
 
         val delay_commit_clean =
           Standard_Thread.delay_first(commit_cleanup_delay max Time.zero) {
             val clean_theories = use_theories_state.change_result(_.clean_theories)
-            if (clean_theories.nonEmpty) resources.clean_theories(session, id, clean_theories)
+            if (clean_theories.nonEmpty) {
+              progress.echo("Removing " + clean_theories.length + " theories ...")
+              resources.clean_theories(session, id, clean_theories)
+            }
           }
 
         Session.Consumer[Session.Commands_Changed](getClass.getName) {
           case changed =>
             if (changed.nodes.exists(dep_theories_set)) {