Support reference bundles.

[cmnbroad]

The main feature implemented here is that a bundle can be used in place of a reference, without executing any code paths that assume that the individual resources are located in the same parent directory (there are a LOT of such code paths, since most of the existing code base makes these assumptions). There are a number of tests added that exist purely to catch any regressions where such assumptions are reintroduced, at lease in the code paths where bundles are enabled.