Update links

- remove links to wiki.chip.org and replace with ones internal to these docs,
  or to dev.smartplatforms.org
Standardize on using Sphinx 'note' directive

- Replacing all **notes** and similar with '.. note::' directive
fix more links and TODOs
remove old schemas

- Removed schemas that were no longer being used, and documentation that went
  with them
- [finishes #42483011]