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The web based Updates controller avoids this issue by completing the migration step as a separate AJAX request from the step where the plugin files are installed, thus allowing for the plugins to be registered by the PluginManager prior to migrations being run. As the plugin:install CLI command runs in a single request, it is necessary to manually register the newly installed plugin prior to running any migrations for the plugin so that any dependencies introduced by the plugin are guaranteed to be available prior to plugin code being run.