If you haven't been following the master branches, there's a new repo flow: flat. All Polymer repos, where possible, have been moved to be sibling dependencies rather than submodules.
If you don't need to hack on polymer itself, it may be a good time to look at polymer-all, which is a meta-repo that contains most of the Polymer repos as a submodule, with the proper dependency hierarchy.
Another big change is the arrival of a polymer build log. Now when polymer is buit, a file named "build.log" will be made that details the build time, sha1 hashes of build files, what commit each repo was at, and the node module versions used during the build.
This should ensure that the builds are repeatable, and you can audit the code used for each build.
All of this comes to the stable branch first thing tomorrow.