autoheader depends on aclocal output, so make the latter run first.
(I was facing bootstrap failures due to different aclocal versions.)

---
 scripts/bootstrap |   20 ++++++++++----------
 1 file changed, 10 insertions(+), 10 deletions(-)

Index: xenomai/scripts/bootstrap
===================================================================
--- xenomai.orig/scripts/bootstrap
+++ xenomai/scripts/bootstrap
@@ -14,16 +14,6 @@ rm -Rf autom4te.cache
 if [ "$?" != "0" ]; then die "removing autom4te.cache"; fi
 echo "done"

-echo -n "running autoheader..."
-autoheader
-if [ "$?" != "0" ]; then die "running autoheader"; fi
-echo "done"
-
-echo -n "running libtoolize..."
-libtoolize -c --automake
-if [ "$?" != "0" ]; then die "running libtoolize"; fi
-echo "done"
-
 echo -n "running aclocal..."
 if test -r acinclude.m4; then
    touch acinclude.m4
@@ -34,6 +24,16 @@ fi
 if [ "$?" != "0" ]; then die "running aclocal"; fi
 echo "done"

+echo -n "running autoheader..."
+autoheader
+if [ "$?" != "0" ]; then die "running autoheader"; fi
+echo "done"
+
+echo -n "running libtoolize..."
+libtoolize -c --automake
+if [ "$?" != "0" ]; then die "running libtoolize"; fi
+echo "done"
+
 echo -n "running autoconf..."
 autoconf
 if [ "$?" != "0" ]; then die "running autoconf"; fi

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