Move GitHub Connect reset to after config-apply

Author: lildude

bin/ghe-restore

@@ -350,11 +350,6 @@ if is_external_database_target_or_snapshot && $SKIP_MYSQL; then
 else
   echo "Restoring MySQL database from ${backup_snapshot_strategy} backup snapshot on an appliance configured for ${appliance_strategy} backups ..."
   ghe-restore-mysql "$GHE_HOSTNAME" 1>&3
-  # Clear GitHub Connect settings stored in the restored database
-  if ! $RESTORE_SETTINGS; then
-    echo "if [ -f /usr/local/share/enterprise/ghe-reset-gh-connect ]; then /usr/local/share/enterprise/ghe-reset-gh-connect -y; fi" |
-    ghe-ssh "$GHE_HOSTNAME" -- /bin/sh 1>&3
-  fi
 fi
 
 if ghe-ssh "$GHE_HOSTNAME" -- 'ghe-config --true app.actions.enabled'; then
@@ -460,6 +455,13 @@ elif $instance_configured; then
   ghe-ssh "$GHE_HOSTNAME" -- "ghe-config-apply" 1>&3 2>&3
 fi
 
+# Clear GitHub Connect settings stored in the restored database.
+# This needs to happen after `ghe-config-apply` to ensure all migrations have run.
+if ! $RESTORE_SETTINGS; then
+  echo "if [ -f /usr/local/share/enterprise/ghe-reset-gh-connect ]; then /usr/local/share/enterprise/ghe-reset-gh-connect -y; fi" |
+  ghe-ssh "$GHE_HOSTNAME" -- /bin/sh 1>&3
+fi
+
 # Start cron. Timerd will start automatically as part of the config run.
 echo "Starting cron ..."
 if $CLUSTER; then