Internals lack flexibility and could perform better.

[iago-lito]

#131 has wrapped previous package code into a first sketch of a stable API for the package.
This previous code is referred to as the Internals module and is getting outdated :

• Not flexible enough to easily feature possible evolutions and features desired by the teams like:
  • Suggestion: replace Matrix{Bool} values with actual directed graphs from Graphs.jl. #77
  • Edges between species actually carry *data*. #82
  • Pre-defined parametrization of the model #69
  • Add non-trophic effects on mortality #31
  • Feature stochastic equations #134
  • .. and more.
• Not performant enough, as the boost option cannot easily propagate to all settings yet, leaving x10 to x100 speedup factors on the table.
  • Benchmarks #34
  • Boost non-trophic interactions. #108

Once #131 has landed, I offer to get deep into the internals and rewrite them entirely to improve performances and make them open to future possible extensions of the model.

But first adress:

• Refactor model API in terms of "Components". #131
• Update doc wrt components API. #135
• Update use cases wrt components API. #136
• Make the repo public. #105 + paper submission
• Simulation output utils are absent from components API. #137
• Components should not be blueprint types. #139
• Docstrings/Doctests are missing from the component API. #140

In particular, a solution to this issue should also be a solution to:

• Edges between species actually carry *data*. #82
• Boost non-trophic interactions. #108
• Update predator preference during the simulation. #150
• Modify internals to make the jacobian computation possible. #179