Mark module as seen only when we have really seen it.

Because a distribution can declare multiple dependencies on the same module,
with an older version appearing before a newer version. If the older version
is already installed, then we would never see that we later need a newer
version that is *not* installed. Discovered when YAML-Tiny started requiring
Test::More 0.94 and 0.99 this week, and the latter was not getting satisfied.