clarified file names;

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/Pure/ROOT.scala	Thu Jul 24 15:01:17 2014 +0200
@@ -0,0 +1,11 @@
+/*  Title:      Pure/ROOT.scala
+    Module:     PIDE
+    Author:     Makarius
+
+Root of isabelle package.
+*/
+
+package object isabelle extends isabelle.Basic_Library
+{
+}
+

--- a/src/Pure/build-jars	Thu Jul 24 14:56:30 2014 +0200
+++ b/src/Pure/build-jars	Thu Jul 24 15:01:17 2014 +0200
@@ -16,6 +16,14 @@
   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
@@ -36,18 +44,10 @@
   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
@@ -67,6 +67,7 @@
   PIDE/text.scala
   PIDE/xml.scala
   PIDE/yxml.scala
+  ROOT.scala
   System/command_line.scala
   System/invoke_scala.scala
   System/isabelle_charset.scala
@@ -83,10 +84,10 @@
   Thy/thy_header.scala
   Thy/thy_info.scala
   Thy/thy_syntax.scala
+  Tools/build.scala
+  Tools/build_console.scala
+  Tools/build_doc.scala
   Tools/check_source.scala
-  Tools/build.scala
-  Tools/build_doc.scala
-  Tools/build_console.scala
   Tools/doc.scala
   Tools/keywords.scala
   Tools/main.scala
@@ -95,7 +96,6 @@
   Tools/simplifier_trace.scala
   Tools/task_statistics.scala
   library.scala
-  package.scala
   term.scala
   term_xml.scala
   "../Tools/Graphview/src/graph_panel.scala"

--- a/src/Pure/package.scala	Thu Jul 24 14:56:30 2014 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
-/*  Title:      Pure/package.scala
-    Module:     PIDE
-    Author:     Makarius
-
-Toplevel isabelle package.
-*/
-
-package object isabelle extends isabelle.Basic_Library
-{
-}
-