Make sure Gem.refresh keeps already loaded gems activated

Previously, calling Gem.refresh made it so all specifications
yielded by Gem::Specification.each had activated = false, even
if the same specs were in Gem.loaded_specs with activated = true.
For consistency, you can either clear Gem.loaded_specs when
refreshing the specifications, or make sure the refreshed
specifications reflect the already loaded gems.  I think the
latter behavior makes more sense.