Makefile.autotools.in: fix autoreconf libtool patching after libtool move

Commit 20f8a7de (support: move libtool patches in support/libtool)
missed the autoreconf variant of the libtool patching, breaking the build
for packages needing both autoreconf and libtool patching.

Signed-off-by: Peter Korsgaard <jacmet@sunsite.dk>