ppgettext should be fixed.
Command documentation actually states:
--ppgettext Group root path for checkout of product. "msgmerge" will post process on the export result based on the current definitionFile in that location
So this change shouldn't result in a fixme, as it is according to the current specification.
I'll make a follow-up commit adding a todo.
Configuration documentation states:
https://www.mediawiki.org/wiki/Help:Extension:Translate/Group_configuration#FILES
FileBasedMessageGroups have method called getSourceFilePath() that could perhaps be suitable.