The recently created repository explorer is not capable of reflecting the path within the repository as part of the application's URL. This makes it much more difficult (if not impossible) to capture the URL to a specific node and use it outside the application such that someone can simply click on the URL to have the explorer open in their browser and be taken exactly to that location.

GitHub.com is a perfect example of how this should work. Git is a hierarchical storage system, and GitHub.com makes it very easy to navigate through that hierarchy. As the user does this, the main outer part of the HTML does not really change, while the inner DIV(s) do change to a) reflect the desired view and b) dynamically change the browser's URL to reflect the location of the node being viewed/edited. See this Stackoverflow question for more details on the latter behavior achievable on most modern browsers; basically it's as simple as:

window.history.pushState("object or string", "Title", "/new-url");

I also think the multi-component look and feel is overkill. Again, GitHub.com's approach shows how easy it is to navigate around the web app without needing a special old-school style tree view, or really any windows/dialogs for other non-reading views.

and pass it in an email, wiki or other mechanism