git source plugin: Emmit the ref-not-in-track warning from validate_cache()

Now that we have Source.validate_cache(), this is a better place to emmit
the ref-not-in-track warning, since it will be emmitted at the earliest
opportunity and not only at Source.stage() or Source.init_workspace().

This also allows us to remove the `self.tracked` local state, and cleanup
some convoluted calling paths, removing some unnecessary parameters from
the usual codepaths and making the plugin overall more readable.