Update user manual reference documentation

[javimed]

Description

This PR updates the Reference guide in the user manual documentation

Documentation compilation

• Verify that documentation compiles without warnings.

Changelog

• Update CHANGELOG.md.

Web optimization & code formatting

• Page references
  • Update /_static/js/redirects.js if necessary (guide).
  • Update /llms.txt if necessary.
• Add or update meta descriptions.
• Use three-space indentation in .rst files.

Writing style

• Use bold for UI elements, italics for key terms and emphasis, and code font for Bash commands, file names, REST paths, and code.
• Follow present tense, active voice, and a semi-formal tone.
• Write short, clear, and concise sentences.