get rid of circular dependencies

[KonradHoeffner]

Dependency cycles (circular dependencies) in the inputs may cause problematic behavior, such as freezing of vitest #407.
We should get rid of them as much as possible without overcomplicating the code but it will take a while and not an immediate priority to do this completely and will require extensive testing afterwards due to major refactoring.
Some of the work has already been done.

In .eslintrc.json, can be set to "import/no-cycle": ["warn"] to show the cycles.
However when not working on the cycles and before they are removed, this can be temporarily set to off, because it may distract from other warnings.

[KonradHoeffner]

As a less strict criterion: While we don't have fixed control flow, like model view controller, it is still not good if in every source file / class we call methods of others without rhyme or reason so we should still make sure that there is a somewhat sensible control flow.

[Yagnap]

Could make progress on this in #437