I added php maintenance/run.php parse.php --parsoid to core, which is one way of running with extensions. But the core parse.php doesn't provide all the features of the Parsoid runner. There's also the --integrated flag to Parsoid's runner, which has probably bit-rotted a bit.

Note that https://gerrit.wikimedia.org/r/c/mediawiki/extensions/Cite/+/1071256 moved Cite to a dependency injection pattern, like the one used in core (and already in other Parsoid extensions).

In order to make this runnable outside core in theory we would need to supply an alternative services object which supplied mock or api-based implementation of the services needed. For example, Cite depends on some configuration variables from core; you could supply an alternate Config service which supplied the correct values based on a either a static site configuration or an API query.