Fix automake warnings

Created by: kbrenneman

This is a series of changes to fix all of the warnings that autoreconf spits out when you run the autogen.sh script.

There's a couple of changes to variable names, but most of these involve getting rid of all of the subdir-objects warnings.

As far as I can tell, if you dont' set the subdir-objects flag, then autoreconf will issue a warning every time there's a source file that's in a different directory from the makefile. And if you do set the subdir-objects flag, then there's no way to reference a source file that's in a parent or sibling directory.

So to deal with that, I rearranged the makefiles so that it will build libtool convenience libraries for everything that needs to be referenced from another directory.