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Adding tutorial in the documentation and fix website generation

Julien Girard-Satabin requested to merge doc/jgirard/tutorial into develop

This merge request adds a tutorial in the documentation. It also removes spurious files in the website folder, fixing #29 and fixes the website generation.

I did not intend to include the tutorial on the website, as embedding jupyter notebooks ask questions on the dedicated resources for the website we cannot address right now.

Technically, it solves #11 , as we do indeed have a website. It only contains some API reference though. Integrating the tutorial on the website can be done later (unless we state that this is a request for this MR to be merged, hence I'll have to do some yml shenanigans).

As the header of the user manual mention ProtoTree and ProtoPNet, I think we can close #3 as well.

Edited by Julien Girard-Satabin

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