Apply transforms correctly to whole packages and modules that depend on multiple packages.

This patch fixes the following two issues:

https://github.com/substack/module-deps/issues/7
https://github.com/substack/module-deps/issues/13

This depends on the following pull requests in dependencies of `module-deps`:

https://github.com/substack/node-resolve/pull/21
https://github.com/shtylman/node-browser-resolve/pull/23

Once in place, package metadata is preserved throughout the resolution process, allowing transforms to be applied correctly to whole modules (as well as addressing an issue of where transforms from multiple dependencies were not respected).