Namespace cleanup

Initial goal: Change references to aliases such as Wikibase\EntityId to their new FQN

Which forced doing: Move classes into Wikibase\Lib\Store to enable
moving away from deprecated class aliases. The updating of references
this caused is the bulk of this commit.

Along the way, this cleanup was also done

* Update refs from SimpleSiteLink to SiteLink
* Decreased visibility of several fields and methods
* Removed a pile clutter docs
* Migrated some highly deprecated code that will break with DM 1.0

Change-Id: I908c43505c3ef66386b123c01cdc40bcba9ef9b8
Merge "Namespace cleanup"