As part of T263762: Make Kartographer extension compatible with Parsoid we moved a lot of code into smaller, independent service classes that can be reused by both parsers. All this code was and still is sufficiently covered by the previously existing PHPUnit tests as well as an extensive set of parser tests. Unfortunately this is not reflected in the coverage report: https://doc.wikimedia.org/cover-extensions/Kartographer.
While there are several easy ways to fix this, we think the best is to write new, clean, pure unit tests for these classes.
Some really trivial classes/methods can be marked with @codeCoverageIgnore.