added update_header tool;

--- a/NEWS	Sun Nov 02 16:39:54 2014 +0100
+++ b/NEWS	Sun Nov 02 16:47:45 2014 +0100
@@ -172,7 +172,8 @@
 before the initial 'theory' command.  Obsolete proof commands 'sect',
 'subsect', 'subsubsect' have been discontinued.  The Obsolete 'header'
 command is still retained for some time, but should be replaced by
-'chapter', 'section' etc. Minor INCOMPATIBILITY.
+'chapter', 'section' etc. (using "isabelle update_header"). Minor
+INCOMPATIBILITY.
 
 * Official support for "tt" style variants, via \isatt{...} or
 \begin{isabellett}...\end{isabellett}. The somewhat fragile \verb or

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/lib/Tools/update_header	Sun Nov 02 16:47:45 2014 +0100
@@ -0,0 +1,60 @@
+#!/usr/bin/env bash
+#
+# Author: Makarius
+#
+# DESCRIPTION: replace obsolete theory header command
+
+
+## diagnostics
+
+PRG="$(basename "$0")"
+
+function usage()
+{
+  echo
+  echo "Usage: isabelle $PRG [FILES|DIRS...]"
+  echo
+  echo "  Options are:"
+  echo "    -s COMMAND   alternative heading command (default 'section')"
+  echo
+  echo "  Recursively find .thy files and replace obsolete theory header commands"
+  echo "  by 'section' (default), or 'chapter', 'subsection', 'subsubsection'."
+  echo
+  echo "  Old versions of files are preserved by appending \"~~\"."
+  echo
+  exit 1
+}
+
+
+## process command line
+
+#options
+
+SECTION="section"
+
+while getopts "s:" OPT
+do
+  case "$OPT" in
+    s)
+      SECTION="$OPTARG"
+      ;;
+    \?)
+      usage
+      ;;
+  esac
+done
+
+shift $(($OPTIND - 1))
+
+
+# args
+
+[ "$#" -eq 0 -o "$1" = "-?" ] && usage
+
+SPECS="$@"; shift "$#"
+
+
+## main
+
+find $SPECS -name \*.thy -print0 | \
+  xargs -0 "$ISABELLE_TOOL" java isabelle.Update_Header "$SECTION"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/Pure/Tools/update_header.scala	Sun Nov 02 16:47:45 2014 +0100
@@ -0,0 +1,40 @@
+/*  Title:      Pure/Tools/update_header.scala
+    Author:     Makarius
+
+Replace theory header command.
+*/
+
+package isabelle
+
+
+object Update_Header
+{
+  def update_header(section: String, path: Path)
+  {
+    val text0 = File.read(path)
+    val text1 =
+      (for (tok <- Outer_Syntax.empty.scan(text0).iterator)
+        yield { if (tok.source == "header") section else tok.source }).mkString
+
+    if (text0 != text1) {
+      Output.writeln("changing " + path)
+      File.write_backup2(path, text1)
+    }
+  }
+
+
+  /* command line entry point */
+
+  def main(args: Array[String])
+  {
+    Command_Line.tool0 {
+      args.toList match {
+        case section :: files =>
+          if (!Set("chapter", "section", "subsection", "subsubsection").contains(section))
+            error("Bad heading command: " + quote(section))
+          files.foreach(file => update_header(section, Path.explode(file)))
+        case _ => error("Bad arguments:\n" + cat_lines(args))
+      }
+    }
+  }
+}

--- a/src/Pure/build-jars	Sun Nov 02 16:39:54 2014 +0100
+++ b/src/Pure/build-jars	Sun Nov 02 16:47:45 2014 +0100
@@ -96,6 +96,7 @@
   Tools/simplifier_trace.scala
   Tools/task_statistics.scala
   Tools/update_cartouches.scala
+  Tools/update_header.scala
   Tools/update_semicolons.scala
   library.scala
   term.scala