more thorough update of options;

--- a/src/Tools/jEdit/src/isabelle.scala	Sat Nov 21 19:04:39 2015 +0100
+++ b/src/Tools/jEdit/src/isabelle.scala	Sat Nov 21 19:27:06 2015 +0100
@@ -187,8 +187,7 @@
     GUI_Thread.require {
       if (continuous_checking != b) {
         PIDE.options.bool(CONTINUOUS_CHECKING) = b
-        PIDE.options_changed()
-        PIDE.editor.flush()
+        PIDE.session.update_options(PIDE.options.value)
       }
     }
 

--- a/src/Tools/jEdit/src/output_dockable.scala	Sat Nov 21 19:04:39 2015 +0100
+++ b/src/Tools/jEdit/src/output_dockable.scala	Sat Nov 21 19:27:06 2015 +0100
@@ -90,8 +90,7 @@
   {
     if (output_state != b) {
       PIDE.options.bool("editor_output_state") = b
-      PIDE.options_changed()
-      PIDE.editor.flush()
+      PIDE.session.update_options(PIDE.options.value)
     }
   }