Propagate IOException where possible when getting refs.
Currently, Repository.getAllRefs() and Repository.getTags() silently
ignores an IOException and instead returns an empty map. Repository
is a public API and as such cannot be changed until the next major
revision change. Where possible, update the internal jgit APIs to
use the RefDatabase directly, since it propagates the error.
Change-Id: I4e4537d8bd0fa772f388262684c5c4ca1929dc4c