When you bin/storage upgrade the first time, we often have adjustments to apply because we've changed keys or column types by adjusting the authority in PHP and letting the adjustment process fix the database.
Currently, we prompt you to apply them. This isn't really a useful prompt if we just initialized storage.
$ ./bin/storage upgrade --namespace breaddog Before running storage upgrades, you should take down the Phabricator web interface and stop any running Phabricator daemons (you can disable this warning with --force). Are you ready to continue? [y/N] y ...<snip many patches>... Database Table Name Issues breaddog_calendar calendar_event userPHID_dateFrom Surplus Key breaddog_calendar calendar_event key_date Missing Key breaddog_file file_transaction_comment key_draft Surplus Key breaddog_harbormaster harbormaster_build key_initiator Missing Key breaddog_herald herald_rule name Better Collation Available breaddog_herald herald_rule key_name Missing Key breaddog_instances instances_instance key_account Missing Key breaddog_instances instances_instance key_oauth Missing Key breaddog_ledger ledger_account key_phid Missing Key breaddog_ledger ledger_merchant key_phid Missing Key breaddog_ledger ledger_payment key_phid Missing Key breaddog_packages packages_package name Better Collation Available breaddog_packages packages_publisher name Better Collation Available breaddog_search search_document key_type Missing Key breaddog_worker worker_archivetask key_modified Missing Key Found 15 issues(s) with schemata, detailed above. You can review issues in more detail from the web interface, in Config > Database Status. To better understand the adjustment workflow, see "Managing Storage Adjustments" in the documentation. MySQL needs to copy table data to make some adjustments, so these migrations may take some time. Fix these schema issues? [y/N]
We could reasonably just --force these to apply, and/or make the help text a little more reassuring for first-time users.