Order of merged paths in App::build (bootstrapping in 1.3)

From the API: App::build -- Build path references. Merges the supplied
$paths with the base paths and the default core paths.

How can I change the order in which the paths are merged, and thus
called?

In 1.2 I used bootstrapping to share controllers, models, views, etc.
across multiple applications, but I could still override the shared
file by creating one locally in an app. The bootstrapping method would
look first in the base path (app), second in the supplied
$controllerPaths array, and third in the core library. Now in 1.3 it
seems the order is supplied path in App::build, then base (app), then
in the core. Any idea how to change this?

-Corie

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