Refactor subgraph runner

[mangas]

Subgraph runner has some code duplication and a lot of if-else-ish code. We should try to improve it by making some concerns more isolated and the error more testable.

This is probably going to require several iterations on different parts but the sooner we start the sooner we finish.

As @lutter pointed out, this last PR added some more code duplication which doesn't help #4916 (comment)