phases: move root phase assignment to it's own function This moves the initial root phase assignment to it's own function. Future patches which make phase calculations lazy will use this function to pre-fill certain phases which can be deduced from the roots.

phases: add invalidate function Phase cache invalidation was spread all over the place. Let's add a function to unify it. Later more will be added to this function.

phases: change phase command change detection A future patch is going to make phase computation lazy, so the phase command can no longer read and diff the entire phase list directly. This changes the phase command to build it's own list for diff purposes.

spanset: remove `.set()` definition All my friends are dead.

generatorset: remove `.set()` definition All my friends are dead.

addset: remove `.set()` definition All my friends are dead.

filteredset: remove `.set()` definition All my friends are dead.

baseset: remove `set()` definition All my friends are dead.