Pull all migration actions together into one place

[waxlamp]

This might be a collection of scripts (or one huge script) in a specific place in the repo, with a pipenv script attached to it.

Currently there is at least one Python script (for patching workspace permission information), and a server startup that syncs the workspace_mapping collection with the databases. If there are other migration things, they should be included in this.

We should also investigate whether the flask migrate command could be used here in some way.

TODO:

• pull register_legacy_workspaces() into a migration script (see Consider extracting register_legacy_workspaces() to an external script #342)
• Add migration for table metadata (see Introduce Table Metadata #484 (comment))