Major docs restructure

[matteopilz]

The restructure mostly focuses on reordering files and sections to allow easier access for new users. It does not include major rewrites of sections.

Describe the change

PR checklist

• [ ] I have added description of the change I'm proposing in the OpenMS Documentation.
• [ ] I have read and followed OpenMS Documentation Contributing guidelines.
• [ ] I have attached a screenshot of the relevant area after this change.
• [ ] CHANGELOG.md is updated.
• [ ] I have added my name in CONTRIBUTING.md.