knowledge: API migration to SQLAlchemy

* Replaces run_sql queries with SQLAchemy query.

* Refactors module in order to move logic from api to model.

* Fixes bibknowledge webinterface kb mapping update.

* NOTE If you are running Invenio 1 and Invenio 2 on top of
  the same database, please use only Invenio 2 knowledge base
  administration interface from now on, in order to ensure
  data consistency.

Signed-off-by: Leonardo Rossi <leonardo.r@cern.ch>