Apply object-oriented principles including a namespace package

[vijayiyer05]

The use of namespaced packages is a growing best practice. It would allow EXTRACT to be installed into any MATLAB installation without any function name collisions.

For instance, there could be a top-level +extract package from which EXTRACT-associated functions could be called unambiguously: >> extract.cell_check

As time permits, further use of object-oriented programming principles might be considered, such as an object model which defines a class consolidating the EXTRACT hyperparameters as class properties.

ℹ️ This issue is a refactor so work on a separate branch/fork is essential

[vijayiyer05]

@dimitri-yatsenko, @yambottle, @manisha-sinha-appasamy : good discussion last week.

We spoke about the motivation for the core goal (package namespacing): this is to help support future integration of EXTRACT into broader frameworks and even potentially managed environments such as the DataJoint services.

I'd also like to give @bahanonu a chance to weigh in. He suggested that package namespacing would improve the EXTRACT integration into CIATAH. He also has used package namespaces for CIATAH itself.

[vijayiyer05]

@yambottle Thanks for the recent(ish) overview of your progress on this Issue.

Here are some suggestions:

• As part of presenting a full vision for the folder org as part of this package refactor, suggest to rename the two root-level folders:

  • "Learning materials" --> "Tutorials"
  • "Template scripts" --> "Examples"

• Rename +externals to +external (matches common convention)

• Rename +helpers into +internal

• Move +debug into +internal*