[migration] reorder system tables / meta-schema migration into bootstrap_migration
Also fix a bug in the backwards-compat eid_type_source method where it
returned an extid (possibly null) instead of a source name.
With these changes, migrating a database from cw 3.12 is now possible.
Closes #4962681
option_group_changed('port', 'main', 'web')
option_group_changed('query-log-file', 'main', 'web')
option_group_changed('profile', 'main', 'web')
option_group_changed('max-post-length', 'main', 'web')