repo-updater: Do not migrate deleted repos to `(repos|projects)` list

Created by: tsenart

This commit is a proposed solution to #3588. It changes the EnabledStateDeprecationMigration so that it doesn't migrate deleted repos, nor repos that would have been deleted on the first syncer run, to an explicit include list (repos in Github and Bitbucket Server, projects in Gitlab).

There were reports of confusion around these repos lists being populated in all external service configurations. The explanation for this is that we previously didn't have a link between repos and the external services that yielded them. Because this migration could not know which external service a repo came from, it added these include and exclude lists to ALL external services of the same kind.

While this safe to do for exclude, we know learned that it wasn't for repos|projects due to these requests to code hosts inquiring about deleted repos consuming rate limit quota. Having this repos list present in every active external service that shared an account / token, accelerated the exhaustion of the rate limit quota.

Fixes #3588