Decide what to do with `atlas_generation/main_script`

[adamltyson]

The idea of this was to have a single script that can run all the atlas generation. We should either:

• Update it to generate all the atlases
• Delete it

cc @viktorpm @alessandrofelder

[alessandrofelder]

My initial suggestion would be to update it (and make it more robust, improve logging document it better)