Quote AC_LANG_PROGRAM to silence new Autoconf warnings and use auxiliary configuration directory.
Use autoreconf instead of manually invoking each tool one by one.  Allow arguments to be passed to autogen.sh.
Update newer INSTALL file.
Remove GNU Build Systems artifacts from .gitignore and ignore the entire auxiliary configuration directory instead.
Fix typo in ACLOCAL_AMFLAGS definition.
Add AM_CPPFLAGS so that includes work in an out-of-tree build.
Remove docdir definition (solves warning: docdir was already defined in condition TRUE, which includes condition DOXYGEN_ENABLE in configure.ac:5.