Ensure active gems are always found

Previously a gem could be loaded from the same file multiple times.
The active version would only be marked in one place so subsequent
loads would not know the gem was already active.

Now we check the loaded specs (when loading a stub) and all specs (when
loading a LockSpecification to ensure the activated flag can be
discovered across all load points.

This allows bin stubs to find the gem version that was activated
instead of the latest version as it can now see active gems.

Fixes #991