diff --git a/src/Pure/Tools/main.scala b/src/Pure/Tools/main.scala
--- a/src/Pure/Tools/main.scala
+++ b/src/Pure/Tools/main.scala
@@ -1,141 +1,151 @@
 /*  Title:      Pure/Tools/main.scala
     Author:     Makarius
 
 Main Isabelle application entry point.
 */
 
 package isabelle
 
 
 import java.lang.{Class, ClassLoader}
 
 
 object Main
 {
   /* main entry point */
 
   def main(args: Array[String])
   {
     if (args.nonEmpty && args(0) == "-init") {
       Isabelle_System.init()
     }
     else {
       val start =
       {
         try {
           Isabelle_System.init()
           Isabelle_Fonts.init()
 
           GUI.init_lafs()
 
 
           /* ROOTS template */
 
           {
             val roots = Path.explode("$ISABELLE_HOME_USER/ROOTS")
             if (!roots.is_file) File.write(roots, """# Additional session root directories
 #
-#   * each line contains one directory entry in Isabelle path notation
+#   * each line contains one directory entry in Isabelle path notation, e.g.
+#
+#       $ISABELLE_HOME/../AFP/thys
+#
+#     for a copy of AFP put side-by-side to the Isabelle distribution
+#
+#   * Isabelle/jEdit provides formal markup for C-hover-click and completion
+#
 #   * lines starting with "#" are stripped
-#   * changes require application restart
+#
+#   * changes require restart of the Isabelle application
 #
 #:mode=text:encoding=UTF-8:
+
+#$ISABELLE_HOME/../AFP/thys
 """)
           }
 
 
           /* settings directory */
 
           val settings_dir = Path.explode("$JEDIT_SETTINGS")
 
           val properties = settings_dir + Path.explode("properties")
           if (properties.is_file) {
             val props1 = split_lines(File.read(properties))
             val props2 = props1.filterNot(_.startsWith("plugin-blacklist.Isabelle-jEdit"))
             if (props1 != props2) File.write(properties, cat_lines(props2))
           }
 
           Isabelle_System.make_directory(settings_dir + Path.explode("DockableWindowManager"))
 
           if (!(settings_dir + Path.explode("perspective.xml")).is_file) {
             File.write(settings_dir + Path.explode("DockableWindowManager/perspective-view0.xml"),
               """<DOCKING LEFT="isabelle-documentation" TOP="" RIGHT="isabelle-theories" BOTTOM="" LEFT_POS="250" TOP_POS="0" RIGHT_POS="250" BOTTOM_POS="250" />""")
             File.write(settings_dir + Path.explode("perspective.xml"),
               XML.header +
 """<!DOCTYPE PERSPECTIVE SYSTEM "perspective.dtd">
 <PERSPECTIVE>
 <VIEW PLAIN="FALSE">
 <GEOMETRY X="0" Y="35" WIDTH="1200" HEIGHT="850" EXT_STATE="0" />
 </VIEW>
 </PERSPECTIVE>""")
           }
 
 
           /* args */
 
           val jedit_settings =
             "-settings=" + File.platform_path(Path.explode("$JEDIT_SETTINGS"))
 
           val jedit_server =
             System.getProperty("isabelle.jedit_server") match {
               case null | "" => "-noserver"
               case name => "-server=" + name
             }
 
           val jedit_options =
             Isabelle_System.getenv_strict("JEDIT_OPTIONS").split(" +")
 
           val more_args =
           {
             args.toList.dropWhile(arg => arg.startsWith("-") && arg != "--") match {
               case Nil | List("--") =>
                 args ++ Array(File.platform_path(Path.explode("$USER_HOME/Scratch.thy")))
               case List(":") => args.slice(0, args.size - 1)
               case _ => args
             }
           }
 
 
           /* environment */
 
           def putenv(name: String, value: String)
           {
             val misc =
               Class.forName("org.gjt.sp.jedit.MiscUtilities", true, ClassLoader.getSystemClassLoader)
             val putenv = misc.getMethod("putenv", classOf[String], classOf[String])
             putenv.invoke(null, name, value)
           }
 
           for (name <- List("ISABELLE_HOME", "ISABELLE_HOME_USER", "JEDIT_HOME", "JEDIT_SETTINGS")) {
             putenv(name, File.platform_path(Isabelle_System.getenv(name)))
           }
           putenv("ISABELLE_ROOT", null)
 
 
           /* properties */
 
           System.setProperty("jedit.home", File.platform_path(Path.explode("$JEDIT_HOME/dist")))
           System.setProperty("scala.home", File.platform_path(Path.explode("$SCALA_HOME")))
           System.setProperty("scala.color", "false")
 
 
           /* main startup */
 
           val jedit =
             Class.forName("org.gjt.sp.jedit.jEdit", true, ClassLoader.getSystemClassLoader)
           val jedit_main = jedit.getMethod("main", classOf[Array[String]])
 
           () => jedit_main.invoke(
             null, Array(jedit_settings, jedit_server) ++ jedit_options ++ more_args)
         }
         catch {
           case exn: Throwable =>
             GUI.init_laf()
             GUI.dialog(null, "Isabelle", GUI.scrollable_text(Exn.message(exn)))
             sys.exit(2)
         }
       }
       start()
     }
   }
 }