Atmos wrapper

[lsoucasse]

This PR reorganizes the Proteus repository and introduces a wrapper function to access the atmosphere submodules (JANUS/AGNI/dummy):

• All atmosphere-related scripts are now in the src/proteus/atmosphere folder.
• The wrapper script wrapper_atmosphere.py is for now very basic: it only copies previous atmosphere sub-loop code lines into a RunAtmosphere function. We might want to improve it through an AtmosphereModel class for instance. Also we might want to change the module import such that it only does the import of the submodule it needs.
• The utils/ and plots/ directories are moved into src/proteus/. It means that the pip install -e . command needs to be run to access associated scripts. The tools folder remains in the root as it gathers notebooks and pre/post-process scripts.

Everything seems OK on the JANUS side but I didn't check everything on the AGNI side. Could you try this @nichollsh?

[timlichtenberg]

I am going to go through this commit as well, I think we should wait for Stef and Harrison to make comments as well, since this is a major reshuffle of folders and structure.