Fix/improve documentation formatting

[majabojarska]

Description

Fixes markdown formatting/indentation issues to properly render via mkdocs:

• Enumeration. Several enumerated lists rendered improperly, as multiple "1." entries:
• Replace sequential enumeration (1. 2. 3. ...) with 1.-based enumeration. The renderer takes care of mapping the correct index to each list element. Generally easier to maintain.
• Improves readability by using admonitions, e.g.:
• Improves consistency of monospace formatting for package/image names.

Validation steps

1. Run make serve.
2. Open the live preview.
3. Inspect the rendered documents relevant to the PR's scope.

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• [x] read the CONTRIBUTING guidelines
• [ ] ~raised a GitHub issue or discussed it on the projects chat beforehand~ Not applicable
• [ ] ~added unit tests~ Not applicable
• [ ] ~added integration tests~ Not applicable
• [x] updated documentation if needed
• [ ] updated CHANGELOG.md