autotools: Improve configure dependency code for finding m4 files

We have an open bug about the warnings issues in builds from an sstate
cache when something like glib-2.0 gets rebuilt. The issue is that
sstate is "clever" and prunes unneeded dependencies out the tree.

For example is X depends on pkgconfig-native but we've already build X
and installed it from sstate, it will not get installed when you build Y
which depends on X.

This patch changes the logic to match the sstate behaviour and prune out
unnecessary dependencies from the scope of aclocal. This in turn removes
the warning about missing manifest files.

The issue is that this patch exposes holes in our DEPENDS in recipes,
specifically that some native tools are not listed, specifically, and
problematically, pkgconfig, gtk-doc and intltool-native in particular.

I've sent out patches against OE-Core that address the bulk of the
issues there however I'm conscious this is probably going to a bug issue
in other layers and may be too annoying to consider at this point. The
other alternative is simply to turn the warning into a debug statement.

I appreciate the code below has commented blocks, this is simply debug
I've left around for now. It will be cleaned from any final version.

Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>

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