Ensure populate sites works for updating existing sites

also:

* add 'en' as language code for special sites,
parts of wikibase depend on there being a language
for all sites.
* improve site matrix parser test

Change-Id: I2f50f40d0a796f03ef78c524bca63018595207e5
(cherry picked from commit e731705a7489a227c43c97282ca51afd2526862e)