Initial clean-up and reorganization of InfrastructureSystems documentation

[kennedy-mindermann]

The existing InfrastructureSystems documentation needs to be cleaned up prior to reorganizing with the new Diataxis format. This includes:

• Upgrading to Documenter > 1.0 and resolving errors to enforce strict compilation
  • Documenter is updated, but make.jl still is only warning, and errors need to be fixed
• Adding .md formatting to the formatter script
• Proof-reading for formatting and misformatted code references
• Adding hyperlinks everywhere