prefer (old) isa-index as provided here, to get exactly the same index layout as in Isabelle2012;
more accurate ROOT/files;

--- a/doc-src/ROOT	Tue Aug 28 15:00:05 2012 +0200
+++ b/doc-src/ROOT	Tue Aug 28 15:07:43 2012 +0200
@@ -343,8 +343,28 @@
     "../proof.sty"
     "../ttbox.sty"
     "../manual.bib"
+    "document/advanced0.tex"
+    "document/appendix0.tex"
+    "document/basics.tex"
+    "document/build"
+    "document/cl2emono-modified.sty"
+    "document/ctl0.tex"
+    "document/documents0.tex"
+    "document/fp.tex"
+    "document/inductive0.tex"
+    "document/isa-index"
+    "document/Isa-logics.eps"
+    "document/Isa-logics.pdf"
+    "document/numerics.tex"
     "document/pghead.eps"
     "document/pghead.pdf"
-    "document/build"
+    "document/preface.tex"
+    "document/protocol.tex"
     "document/root.tex"
+    "document/rules.tex"
+    "document/sets.tex"
+    "document/tutorial.sty"
+    "document/typedef.pdf"
+    "document/typedef.ps"
+    "document/types0.tex"
 

--- a/doc-src/TutorialI/document/build	Tue Aug 28 15:00:05 2012 +0200
+++ b/doc-src/TutorialI/document/build	Tue Aug 28 15:07:43 2012 +0200
@@ -22,7 +22,7 @@
 "$ISABELLE_TOOL" latex -o bbl
 "$ISABELLE_TOOL" latex -o "$FORMAT"
 "$ISABELLE_TOOL" latex -o "$FORMAT"
-"$ISABELLE_HOME/doc-src/sedindex" root
+./isa-index root
 [ -f root.out ] && "$ISABELLE_HOME/doc-src/fixbookmarks" root.out
 "$ISABELLE_TOOL" latex -o "$FORMAT"
 "$ISABELLE_TOOL" latex -o "$FORMAT"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/doc-src/TutorialI/document/isa-index	Tue Aug 28 15:07:43 2012 +0200
@@ -0,0 +1,23 @@
+#! /bin/sh
+#
+#sedindex - shell script to create indexes, preprocessing LaTeX's .idx file
+#
+#  puts strings prefixed by * into \tt font
+#    terminator characters for strings are |!@{}
+#
+# a space terminates the \tt part to allow \index{*notE theorem}, etc.
+#
+# note that makeindex uses a dboule quote (") to delimit special characters.
+#
+# change *"X"Y"Z"W  to  "X"Y"Z"W@{\tt "X"Y"Z"W}
+# change *"X"Y"Z    to  "X"Y"Z@{\tt "X"Y"Z}
+# change *"X"Y      to  "X"Y@{\tt "X"Y}
+# change *"X        to  "X@{\tt "X}
+# change *IDENT  to  IDENT@{\tt IDENT}  
+#    where IDENT is any string not containing | ! or @
+# FOUR backslashes: to escape the shell AND sed
+sed -e "s~\*\(\".\".\".\".\)~\1@\\\\isa {\1}~g
+s~\*\(\".\".\".\)~\1@\\\\isa {\1}~g
+s~\*\(\".\".\)~\1@\\\\isa {\1}~g
+s~\*\(\".\)~\1@\\\\isa {\1}~g
+s~\*\([^ |!@{}][^ |!@{}]*\)~\1@\\\\isa {\1}~g" $1.idx | makeindex -c -q -o $1.ind

--- a/doc-src/TutorialI/isa-index	Tue Aug 28 15:00:05 2012 +0200
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-#! /bin/sh
-#
-#sedindex - shell script to create indexes, preprocessing LaTeX's .idx file
-#
-#  puts strings prefixed by * into \tt font
-#    terminator characters for strings are |!@{}
-#
-# a space terminates the \tt part to allow \index{*notE theorem}, etc.
-#
-# note that makeindex uses a dboule quote (") to delimit special characters.
-#
-# change *"X"Y"Z"W  to  "X"Y"Z"W@{\tt "X"Y"Z"W}
-# change *"X"Y"Z    to  "X"Y"Z@{\tt "X"Y"Z}
-# change *"X"Y      to  "X"Y@{\tt "X"Y}
-# change *"X        to  "X@{\tt "X}
-# change *IDENT  to  IDENT@{\tt IDENT}  
-#    where IDENT is any string not containing | ! or @
-# FOUR backslashes: to escape the shell AND sed
-sed -e "s~\*\(\".\".\".\".\)~\1@\\\\isa {\1}~g
-s~\*\(\".\".\".\)~\1@\\\\isa {\1}~g
-s~\*\(\".\".\)~\1@\\\\isa {\1}~g
-s~\*\(\".\)~\1@\\\\isa {\1}~g
-s~\*\([^ |!@{}][^ |!@{}]*\)~\1@\\\\isa {\1}~g" $1.idx | makeindex -c -q -o $1.ind