docs: add note for index.php change

[kenjis]

Description I saw a YouTube video that a dev had moved index.php to the project root. Also this description is on the README file, but not in the User Guide upgrading section.

aChecklist:

• [x] Securely signed commits
• [] Component(s) with PHPDoc blocks, only if necessary or adds value
• [] Unit testing, with >80% coverage
• [x] User guide updated
• [] Conforms to style guide