The EventLogging extension manages the Schema namespace on metawiki. We should use the same config wgEventLoggingSchemas config switch we use to handle backwards compatibility to add a deprecation/migration notice to schemas on metawiki.
That is, we edit EventLogging's includes/ApiJsonSchema.php, includes/JsonSchemaContent.php, and or includes/JsonSchemaContentHandler.php to render a deprecation notice at the schema's wikipage if $wgEventLoggingSchemas['SchemaName'] is a string.
This would help automate the migration process and hopefully avoid confusion when folks might attempt to edit their schemas on wiki after they have been migrated to the git repo.