Derek furst/hubmap sdk

[DerekFurstPitt]

Major Updates:

• Restructured files such that all hubmap-sdk related files are in one directory and all hubmap-clt related files are in one directory
• Changed _layouts.html to reflect the above changes. Added leading slashes to assays, apis, and sdk.

Minor Updates:

Updated hubmap-clt docs to reflect new changes. Updated hubmap-sdk docs to include jupyter notebook.

[DerekFurstPitt]

@shirey I'm adding you as a reviewer to this update to software docs. Normally since its just the documentation I wouldn't bother, but i've changed some file structure and edited the page layout so it would be good to make sure I didn't do something improperly