Migration tool should use one transaction not a transaction per user

[matrixbot]

This issue was originally created by @hughns at matrix-org/matrix-authentication-service#2268.

Currently we have a hangover from an incremental migration mode that was never completed.

Instead we should be doing a single transaction and only committing it on success.

[reivilibre]

Closed by #3895 which now uses multiple parallel transactions, but not one per user