regen.sh propagates settings inappropriately

When running "regen.sh", we've observed that some values in "civicrm_settings" may be inappropriately propagated from the local database into the generated databases.

There are pieces in the current theory:

1. When regen.sh calls "System.flush", it repopulates all the settings.
2. Some dev env's (esp. buildkit) have settings prepopulated via global $civicrm_settings.

There are currently some hacky bits in regen.sh which clear a list of specific settings. We should try to make this a bit cleaner.