docs: refresh CLI and minimega documentation

[GhostofGoes]

Description

Refresh the phēnix documentation to match the current CLI and minimega documentation:

• Document phenix mm, including command execution, namespaces, console attachment, C2, and socket configuration.
• Add global CLI flag reference and update command help output.
• Expand experiment creation, GUI upload, and common workflow guidance.
• Clarify VM snapshot, backing image, and vm info documentation.
• Update user administration resources and built-in roles.
• Remove legacy prompt formatting, add syntax highlighting, and update minimega links.

Related Issue

Not applicable.

Type of Change

• Bugfix
• New feature
• Documentation update
• Other (please describe):

Checklist

• This PR conforms to the process detailed in the Contributing Guide.
• I have included no proprietary/sensitive information in my code.
• I have performed a self-review of my code.
• I have commented my code, particularly in hard-to-understand areas.
• I have made corresponding changes to the documentation.
• My changes generate no new warnings.
• I have tested my code.

Additional Notes

Validation: make lint passes. The branch was rebased onto the latest upstream/main before opening this pull request.