flex: Patch Makefile.in instead of Makefile.am

This avoids the following error when building under ubuntu 18.04
which has a never version of automake:

configure.ac:31: error: version mismatch.  This is Automake 1.15.1,
configure.ac:31: but the definition used by this AM_INIT_AUTOMAKE
configure.ac:31: comes from Automake 1.15.  You should recreate
configure.ac:31: aclocal.m4 with aclocal and run automake again.