Docs: change all notes with mdbook-alerts

[jenninikko]

Description of changes

Notes, Tips, Warnings, and others are updated according to the GitHub Flavored Markdown's Alerts syntax.

Checklist for things done

• [ ] Summary of the proposed changes in the PR description
• [ ] More detailed description in the commit message(s)
• [ ] Commits are squashed into relevant entities - avoid a lot of minimal dev time commits in the PR
• [x] Contribution guidelines followed
• [x] Ghaf documentation updated with the commit - https://tiiuae.github.io/ghaf/
• [ ] PR linked to architecture documentation and requirement(s) (ticket id)
• [ ] Test procedure described (or includes tests). Select one or more:
  • [ ] Tested on Lenovo X1 x86_64
  • [ ] Tested on Jetson Orin NX or AGX aarch64
  • [ ] Tested on Polarfire riscv64
• [ ] Author has run nix flake check --accept-flake-config and it passes
• [ ] All automatic Github Action checks pass - see actions
• [ ] Author has added reviewers and removed PR draft status

Testing