Safely create alembic_version table and add the correct stamps

[wgresshoff]

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Description

After a fresh setup of an InvenioRDM instance the alembic_version table was missing which leads to problems when migrating to a newer version. This PR adds a transaction context around the table creation and makes sure the correct connection is used, thus avoiding working in a connection ghost that never got committed.
This version reenables the cli tests.

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[wgresshoff]

Replaces #192