Cleanup several minor autotools warnings

This PR fixes several minor warnings when running `./autogen.sh`:
 * Replace `INCLUDES` with `AM_CPPFLAGS`, which is at least 11 years old now.
 * Update `AC_INIT` and `AM_INIT_AUTOMAKE` calls (probably at least 12 years old.)
 * Fix warnings about missing `AC_LANG_SOURCE` calls, which weren't exactly true. The quoting just made it seem missing to `autoconf`.

Unfortunately, there is still a warning about `CC` being overridden in several places. I don't think there's any easy way to get rid of that one.

One thing I haven't done is update `Makefile.in` and `configure`, for two reasons:
 * I don't use the same version of `autoconf` and `automake` as you. It would bloat the diff a lot to include them, and they might just change back the next time one of you regenerates it.
 * Generated files should not be in version control.