Allow shrubs & trees' model structure to be accessible in the patterns

[OmarShehata]

In the original entwined you can access cubes just as a global list, or you can target specific pieces of structures, such as individual branches for trees, or individual rods for shrubs.

Right now this isn't possible just because the code doesn't store which cubes are in which structure.

I made a change in this commit 6b93fc5 to fix this for fairy circles. This:

1. Updates the fairy circle model to store a list of cubes in the mini cluster, and store a list of mini clusters in the overall model
2. Updates Model.js to store a list of fairyCircles, in addition to storing all of its cubes
3. Updates PatternBase.js so that all patterns can access a reference to the model

To make this work for trees/shrubs you would need to do steps 1 & 2 for them.