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
@@ -1,144 +1,159 @@
 /*  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])
   {
     val start =
     {
       try {
         Isabelle_System.init()
         GUI.install_fonts()
 
 
+        /* 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
+#   * lines starting with "#" are stripped
+#   * changes require application restart
+#
+#:mode=text:encoding=UTF-8:
+""")
+        }
+
+
         /* 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.mkdirs(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="" TOP="" RIGHT="isabelle-documentation" BOTTOM="" LEFT_POS="0" TOP_POS="0" RIGHT_POS="250" BOTTOM_POS="250" />""")
           File.write(settings_dir + Path.explode("perspective.xml"),
             """<?xml version="1.0" encoding="UTF-8" ?>
 <!DOCTYPE PERSPECTIVE SYSTEM "perspective.dtd">
 <PERSPECTIVE>
 <VIEW PLAIN="FALSE">
 <GEOMETRY X="0" Y="35" WIDTH="1072" HEIGHT="787" 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
           }
         }
 
 
         /* main startup */
 
         update_environment()
 
         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")
 
         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()
   }
 
 
   /* adhoc update of JVM environment variables */
 
   def update_environment()
   {
     val update =
     {
       val isabelle_home = Isabelle_System.getenv("ISABELLE_HOME")
       val isabelle_home_user = Isabelle_System.getenv("ISABELLE_HOME_USER")
       val jedit_home = Isabelle_System.getenv("JEDIT_HOME")
       val jedit_settings = Isabelle_System.getenv("JEDIT_SETTINGS")
 
       (env0: Any) => {
         val env = env0.asInstanceOf[java.util.Map[String, String]]
         env.put("ISABELLE_HOME", File.platform_path(isabelle_home))
         env.put("ISABELLE_HOME_USER", File.platform_path(isabelle_home_user))
         env.put("JEDIT_HOME", File.platform_path(jedit_home))
         env.put("JEDIT_SETTINGS", File.platform_path(jedit_settings))
         env.remove("ISABELLE_ROOT")
       }
     }
 
     classOf[java.util.Collections].getDeclaredClasses
       .find(c => c.getName == "java.util.Collections$UnmodifiableMap") match
     {
       case Some(c) =>
         val m = c.getDeclaredField("m")
         m.setAccessible(true)
         update(m.get(System.getenv()))
 
         if (Platform.is_windows) {
           val ProcessEnvironment = Class.forName("java.lang.ProcessEnvironment")
           val field = ProcessEnvironment.getDeclaredField("theCaseInsensitiveEnvironment")
           field.setAccessible(true)
           update(field.get(null))
         }
 
       case None =>
         error("Failed to update JVM environment -- platform incompatibility")
     }
   }
 }