Make repo directory structure match website

[troyraen]

Our repo directory structure is quite different than the rendered website. We've put a lot of thought into the website TOC structure and we should change the repo structure to match it. This is especially important now that these notebooks are about to be pulled into Fornax.

This will involve:

• Move the files
• Update toc.yml
• Update deployed_notebooks_manifest.in
• Update all files in the directory ignore_tutorials
• Check for any hardwired cross links and change them to use internal label references

[troyraen]

@bsipocz if I missed anything in the task list above, please add it.

[bsipocz]

I believe there are still a lot of hard wired cross links (as opposed to internal label referencing), so cross links should be updated, too (ideally the build should pick those issues up and complain, but as we saw with the orphan pages, that may not always happen)