This should help users with the common issue of patching the wrong place.
Also took the opportunity of using proper links in the monkeypatch introduction.
Related to #10216
Co-authored-by: Ran Benita <ran@unusedvar.com>
Moved various documents into subdirectories, how-to and
reference.
Updated multiple links to use `:ref:` instead of `:doc:`,
meaning that files can henceforth be moved around without
breaking references.