So after a little chatting with Cyrille, and looking thru lots of various issues in deploying projects, I came up with something that I think is a solution for including libs like list-abs, mapping, etc. as a folder then using namespace prefixes (something that has been supported for a very long time in all versions of Pd).
Basically, one reason to include a library of abstractions with a project is to make sure that the project will continue to work on new versions of Pd and in many people's different installs. One key thing is getting the right code when you load an object with a name. For example, when you type [scale], and you get the one you want. One key problem here is that binaries will always override abstractions. So if you make an abstraction called threshold.pd in your project, and someone's install or some version of Pd includes a 'threshold' binary, you will not be able to load your threshold.pd in anyway on that setup.
So if you use a namespace prefix, then the binary would have to be in a folder of the same name and have the same name in order to prevent the abstraction from loading. So the question I wanted to answer was an easy way to support using folders for namespaces while including the library with the project. So here's the solution i came up with, you make a 'lib' folder in your project, stick the libraries as folders in 'lib', then use [declare -path lib]. Here's an example:
http://puredata.info/Members/hans/vanilla_libdir.tar.bz2
.hc