Fix the updating of `:git`, `:svn`, and `:hg` dependencies when updating all pods.

Closes https://github.com/CocoaPods/CocoaPods/issues/2859.
[CHANGELOG] Fix formatting
Do not rely on *~/.cocoapods* being present.
Spec for resilience of SourcesManager against non-existing repos
directory.
[CHANGELOG] Add entry for 397b991