Refactor: Remove parent() and root()

[psakievich]

Nalu-Wind propagates a structure where objects contain pointers to their parent() and root() objects. This design makes it very difficult to unit test because it creates a object dependency chain from low level data structures to the highest level.

I propose we work to remove these and instead just add object references to the functions that actually use parent() and root() functions. From my initial review it looks like the number of uses of these functions is dwarfed by the number of objects that have them.

Creating this issue to allow others to weigh in and to track the PR's as I work to remove this design from nalu-wind.

[sayerhs]

@psakievich this is a good idea. At the very least, we should prevent requiring parent/root at construction stage. To ease transition, may be provide registerParent or setParent method to inject hierarchy where necessary, so that things that depend on parent() root() can still work while code is being updated.

[psakievich]

Thanks @sayerhs! This is an excellent suggestion.