PR Summary

This fixes:

• the top-level document of the PDF, contents was removed in DOC: more site re-org #21251.
• the tree for the installation docs, which had Source/FAQ before the Installation Guide
• add Chapters to the ToC, which previously (in 3.5) showed only the handful of Parts
• swaps tutorials/examples and general sections in user guide

Fixes #21655

PR Checklist

Tests and Styling

• [n/a] Has pytest style unit tests (and pytest passes).
• Is Flake 8 compliant (install flake8-docstrings and run flake8 --docstring-convention=all).

Documentation

• [n/a] New features are documented, with examples if plot related.
• [n/a] New features have an entry in doc/users/next_whats_new/ (follow instructions in README.rst there).
• [n/a] API changes documented in doc/api/next_api_changes/ (follow instructions in README.rst there).
• Documentation is sphinx and numpydoc compliant (the docs should build without error).