diff --git a/src/Pure/package.scala b/src/Pure/ROOT.scala
rename from src/Pure/package.scala
rename to src/Pure/ROOT.scala
--- a/src/Pure/package.scala
+++ b/src/Pure/ROOT.scala
@@ -1,11 +1,11 @@
-/*  Title:      Pure/package.scala
+/*  Title:      Pure/ROOT.scala
     Module:     PIDE
     Author:     Makarius
 
-Toplevel isabelle package.
+Root of isabelle package.
 */
 
 package object isabelle extends isabelle.Basic_Library
 {
 }
 
diff --git a/src/Pure/build-jars b/src/Pure/build-jars
--- a/src/Pure/build-jars
+++ b/src/Pure/build-jars
@@ -1,256 +1,256 @@
 #!/usr/bin/env bash
 #
 # Author: Makarius
 #
 # build-jars - build Isabelle/Scala
 #
 # Requires proper Isabelle settings environment.
 
 ## sources
 
 declare -a SOURCES=(
   Concurrent/consumer_thread.scala
   Concurrent/counter.scala
   Concurrent/event_timer.scala
   Concurrent/future.scala
   Concurrent/mailbox.scala
   Concurrent/simple_thread.scala
   Concurrent/synchronized.scala
+  GUI/color_value.scala
+  GUI/gui.scala
+  GUI/gui_thread.scala
+  GUI/html5_panel.scala
+  GUI/jfx_thread.scala
+  GUI/popup.scala
+  GUI/system_dialog.scala
+  GUI/wrap_panel.scala
   General/antiquote.scala
   General/bytes.scala
   General/completion.scala
   General/exn.scala
   General/file.scala
   General/graph.scala
   General/graphics_file.scala
   General/linear_set.scala
   General/long_name.scala
   General/multi_map.scala
   General/output.scala
   General/path.scala
   General/position.scala
   General/pretty.scala
   General/properties.scala
   General/scan.scala
   General/sha1.scala
   General/symbol.scala
   General/time.scala
   General/timing.scala
+  General/untyped.scala
   General/url.scala
-  General/untyped.scala
   General/word.scala
   General/xz_file.scala
-  GUI/color_value.scala
-  GUI/gui.scala
-  GUI/gui_thread.scala
-  GUI/html5_panel.scala
-  GUI/jfx_thread.scala
-  GUI/popup.scala
-  GUI/system_dialog.scala
-  GUI/wrap_panel.scala
   Isar/keyword.scala
   Isar/outer_syntax.scala
   Isar/parse.scala
   Isar/token.scala
   ML/ml_lex.scala
   PIDE/command.scala
   PIDE/document.scala
   PIDE/document_id.scala
   PIDE/editor.scala
   PIDE/markup.scala
   PIDE/markup_tree.scala
   PIDE/protocol.scala
   PIDE/prover.scala
   PIDE/query_operation.scala
   PIDE/resources.scala
   PIDE/session.scala
   PIDE/text.scala
   PIDE/xml.scala
   PIDE/yxml.scala
+  ROOT.scala
   System/command_line.scala
   System/invoke_scala.scala
   System/isabelle_charset.scala
   System/isabelle_font.scala
   System/isabelle_process.scala
   System/isabelle_system.scala
   System/options.scala
   System/platform.scala
   System/posix_interrupt.scala
   System/system_channel.scala
   System/utf8.scala
   Thy/html.scala
   Thy/present.scala
   Thy/thy_header.scala
   Thy/thy_info.scala
   Thy/thy_syntax.scala
-  Tools/check_source.scala
   Tools/build.scala
+  Tools/build_console.scala
   Tools/build_doc.scala
-  Tools/build_console.scala
+  Tools/check_source.scala
   Tools/doc.scala
   Tools/keywords.scala
   Tools/main.scala
   Tools/ml_statistics.scala
   Tools/print_operation.scala
   Tools/simplifier_trace.scala
   Tools/task_statistics.scala
   library.scala
-  package.scala
   term.scala
   term_xml.scala
   "../Tools/Graphview/src/graph_panel.scala"
   "../Tools/Graphview/src/layout_pendulum.scala"
   "../Tools/Graphview/src/main_panel.scala"
   "../Tools/Graphview/src/model.scala"
   "../Tools/Graphview/src/mutator_dialog.scala"
   "../Tools/Graphview/src/mutator_event.scala"
   "../Tools/Graphview/src/mutator.scala"
   "../Tools/Graphview/src/popups.scala"
   "../Tools/Graphview/src/shapes.scala"
   "../Tools/Graphview/src/visualizer.scala"
 )
 
 
 ## diagnostics
 
 PRG="$(basename "$0")"
 
 function usage()
 {
   echo
   echo "Usage: isabelle $PRG [OPTIONS]"
   echo
   echo "  Options are:"
   echo "    -f           fresh build"
   echo "    -t           test separate compilation of PIDE"
   echo
   exit 1
 }
 
 function fail()
 {
   echo "$1" >&2
   exit 2
 }
 
 [ -z "$ISABELLE_HOME" ] && fail "Missing Isabelle settings environment"
 
 
 ## process command line
 
 # options
 
 FRESH=""
 TEST_PIDE=""
 
 while getopts "ft" OPT
 do
   case "$OPT" in
     f)
       FRESH=true
       ;;
     t)
       TEST_PIDE=true
       ;;
     \?)
       usage
       ;;
   esac
 done
 
 shift $(($OPTIND - 1))
 
 
 # args
 
 [ "$#" -ne 0 ] && usage
 
 
 ## build
 
 TARGET_DIR="$ISABELLE_HOME/lib/classes"
 TARGET="$TARGET_DIR/Pure.jar"
 
 declare -a PIDE_SOURCES=()
 declare -a PURE_SOURCES=()
 
 for DEP in "${SOURCES[@]}"
 do
   if grep "Module:.*PIDE" "$DEP" >/dev/null
   then
     PIDE_SOURCES["${#PIDE_SOURCES[@]}"]="$DEP"
   else
     PURE_SOURCES["${#PURE_SOURCES[@]}"]="$DEP"
   fi
 done
 
 declare -a UPDATED=()
 
 if [ -n "$FRESH" ]; then
   OUTDATED=true
 else
   OUTDATED=false
   if [ ! -e "$TARGET" ]; then
     OUTDATED=true
   else
     for DEP in "${SOURCES[@]}"
     do
       [ ! -e "$DEP" ] && fail "Missing file: $DEP"
       [ "$DEP" -nt "$TARGET" ] && {
         OUTDATED=true
         UPDATED["${#UPDATED[@]}"]="$DEP"
       }
     done
   fi
 fi
 
 if [ "$OUTDATED" = true ]
 then
   echo "### Building Isabelle/Scala ..."
 
   [ "${#UPDATED[@]}" -gt 0 ] && {
     echo "Changed files:"
     for FILE in "${UPDATED[@]}"
     do
       echo "  $FILE"
     done
   }
 
   rm -rf classes && mkdir classes
 
   SCALAC_OPTIONS="$ISABELLE_SCALA_BUILD_OPTIONS -d classes"
 
   (
     classpath "$ISABELLE_JDK_HOME/jre/lib/jfxrt.jar"
     classpath classes
     export CLASSPATH="$(jvmpath "$ISABELLE_CLASSPATH")"
 
     if [ "$TEST_PIDE" = true ]; then
       isabelle_scala scalac $SCALAC_OPTIONS "${PIDE_SOURCES[@]}" || \
         fail "Failed to compile PIDE sources"
       isabelle_scala scalac $SCALAC_OPTIONS "${PURE_SOURCES[@]}" || \
         fail "Failed to compile Pure sources"
     else
       isabelle_scala scalac $SCALAC_OPTIONS "${PIDE_SOURCES[@]}" "${PURE_SOURCES[@]}" || \
         fail "Failed to compile sources"
     fi
   ) || exit "$?"
 
   mkdir -p "$TARGET_DIR" || fail "Failed to create directory $TARGET_DIR"
 
   pushd classes >/dev/null
 
   CHARSET_SERVICE="META-INF/services/java.nio.charset.spi.CharsetProvider"
   mkdir -p "$(dirname "$CHARSET_SERVICE")"
   echo isabelle.Isabelle_Charset_Provider > "$CHARSET_SERVICE"
 
   cp "$ISABELLE_HOME/lib/logo/isabelle_transparent-32.gif" isabelle/.
   cp "$ISABELLE_HOME/lib/logo/isabelle_transparent.gif" isabelle/.
 
   isabelle_jdk jar cfe "$(jvmpath "$TARGET")" isabelle.Main META-INF isabelle || \
     fail "Failed to produce $TARGET"
 
   popd >/dev/null
 
   rm -rf classes
 fi