When you go to Documentation and click “View the entire table of contents” everything is as it should AFAIK. But if you jump further from there you will see content structure on the left is not right:
1. Getting Started 1.1. Upgrading Your Package 1.2. Upgrading Your UI Theme Or Package Selectors 1.3. Upgrading Your Syntax Theme 1.4. Summary
Those belong to 5th chapter (which is missing from the content list) and instead it should be:
1. Getting Started 1.1 Why Atom 1.2 Installing Atom 1.3 Atom Basics 1.4 Summary
Also from the documentation the “Getting started” has a wrong target too: Upgrading Your Package.