Rework API reference folders

[seesharprun]

This pull request reworks the API reference folders to prepare them ingestion into the documentation engine. The following changes are made (with rationalizations):

• Removal of root index.md and TOC.yml
  • These are auto-generated by the documentation engine. There's no need to maintain a seperate file and landing page here since the documentation engine builds this dynamically.
• Removal of the per-folder index.md files
  • These are auto-generated by the documentation engine. Keeping a manual Markdown file will increase the possibility of error and the amount of manual work required to add a new reference file since the author will need to find and update all relevant index.md files.
• Addition of _metadata.description.md for each folder. These are Markdown partial files that are picked up by the documentation engine to add a description to the dynamically generated pages. The underscore ensures they are at the "top" of any IDE. The longer name is descriptive enough for new contributors to understand what this file does.
• Add missing folders. There are missing folders in the "operators" section and no folders in the "commands" section.
• Update README