attached you'll find the debdiff of my proposed fix. I choose to remove
the generator line after the build. The other approach to modify the m4
and don't write the generator line in the first place was more intrusive
because of the needed autoreconf.
PS: I also uploaded to mentors if you prefer to grab the already patched
diff -Nru isl-0.08/debian/changelog isl-0.08/debian/changelog
--- isl-0.08/debian/changelog 2011-12-15 17:50:34.000000000 +0100
+++ isl-0.08/debian/changelog 2012-06-27 21:02:10.000000000 +0200
@@ -1,3 +1,11 @@
+isl (0.08-1.1) unstable; urgency=low
+ * Non-maintainer upload.
+ * Note about stdint.h generator differs among architectures
+ and breaks multiarch (Closes: #658841)
+ -- Gregor Jasny <firstname.lastname@example.org> Wed, 27 Jun 2012 21:00:51 +0200
isl (0.08-1) unstable; urgency=low