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Import manuals v4.2

Tomas Lovato requested to merge import-manuals-v4.2 into main

This is an import and clean up of the NEMO manuals (~NEMO, TOP, SI³ ) in the last version of the code before the clean up of main.

I further cleaned up the repository and reduced the number of duplicated figure files (we should decide to use only one format!)

Edited by Tomas Lovato

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