More pedagogical notebeooks

[glyg]

Remark from openjournals/joss-reviews#2973 (comment)

My main concern is the lack of gradual difficulty in the tutorials : reproducing research results is great, but gently steering the user might be missing.

While example 5 is simple as claimed, example 2 is rather complex. To engage scientists to use the software, step-by-step tutorial, or a better gradation of difficulty in the notebook examples, seem required to smoothen the steep learning curve.

[glyg]

New organisation:

• Bases

Bases

Creation

Data structure

Specification

I/O

• Geometry

Geometry

2D

2.5D

Closed 2.5D

Monolayer

Closed Monolayer

Bulk

• Visuallization

Visuallization

Draw specs (document callable "color" spec)

2D

3D

• Effectors & Models

Effectors & Models

TODO (from the Energy min & qsolver nbs)

• Solvers

Solvers

History

Quasistatic

Euler

• Division and rearangements

Division and rearangements

Cell division in2 & 3D

Type 1 & I-O-H

Rosettes & atomic rearangements

• EventManager
  TODO (see explain event manager #6)