Need to fix warnings from automake before deprecated features get retired

All of our configure.ac produce the following (or equivalent) warnings:
<pre>
configure.ac:28: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated. For more info, see:
configure.ac:28: http://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
</pre>
and many instances of
<pre>
warning: source file '$(srcdir)/../../libutils/statistics.c' is in a subdirectory,
but option 'subdir-objects' is disabled
</pre>
for diverse files, not just the one mentioned here.
The documentation overtly warns that support for the deprecated INIT may be retracted some day.
We should aim to fix this sooner rather than later, so that we don't get caught out by that.

See
https://github.com/cfengine/core/pull/1998
for the fix I came up with on reading the automake documentation; however, this changed lots of details in the generated Makefiles and broke the build.
We'll need someone more familiar with automake to look into this if we're to fix it cleanly.