db: drop SA caching_query and FromCache, and thus sql_cache_short beaker cache

It is not a good idea to have dead ORM objects. If we want caching, we should
do it explicit.

It is unknown how much this cache helps, but we can profile and introduce
better caching of simple data where relevant.

codingstyle: trivial whitespace fixes

Reported by flake8.

db: use consistent key/index/constraint names when creating database

This simplifies future Alembic upgrades/downgrades.
http://alembic.zzzcomputing.com/en/latest/naming.html

A future changeset will update old databases to match this naming
convention.

Bump SQLAlchemy minimum version to 1.0, required for naming_convention
support.

Second step in two-part process to rename directories.
This is the actual directory rename.