V.2.0 upgrades

Here is an attempt to fill inn the gaps of the upgrades from v.1.x to v.2.0.

Running alembic after applying these on a master installation, gave the following output:
https://gist.github.com/jalavik/66d909e00d12ee2be3fe

Most of it are not applicable, except maybe the column change in the `tag` table, but I am not sure if this one is necessary..

Touches #1613
Ah indeed I have not looked at part one. I guess some of that is regarding Invenio demosite overlay and some on the individual module model level. It fear it is a bigger job to be sure, perhaps we can delegate part one somehow to more people? Can for example be a candidate for triage meeting.