Deprecate forked and patched bundle db persistence managers

We have several forked persistence managers in our code base. These were added in order to override the consistency checking behavior from the jr bundle db pm. This customized behavior adds two functionalities: referential integrity checking and fixing orphaned nodes. Fixing orphaned nodes has since been added to the jr consistency checker. Referential integrity checking is supported by our standalone consistency checker. Since we currently don't recommend to run the consistency check in embedded mode, this patched and forked code should never be useful.