Move 3 newPackage options to beginDocumentation

[mahrud]

This is a draft for now to see what breaks. Comments welcome.

• fixed newPackage to permit terminal null entries
• moved 3 newPackage options to beginDocumentation
• adjusted existing packages with optional components
• corrected package options in TropicalTorics
• removed FirstPackage stuff from Polymake.m2
• unexported two undefined gfanInterface symbols

Closes #3369.

[mahrud]

For now, I just wanted to make sure all tests passed, but I would like to simplify this further before moving it out of draft mode. Here are a few goals, but feel free to add more:

• [ ] keep beginDocumentation() simple, ideally one option only.
• [ ] maybe allow use of cached examples opportunistically, or even provide a function for generating a single cached example, so we can cache only the necessary examples (e.g. realrank is the only one from CoincidenceRootLoci that needs to be cached)
• [ ] simplify the logic in the background, maybe debug mystery issue I described above with tests disappearing after beginDocumentation()
• [ ] think about whether CacheExampleOutputs should be transitive.
• [ ] think about whether readPackage should know whether optional dependencies are present, because with this PR it will not
• [ ] maybe have one distinguished package for each optional dependency so we don't check for existence of the same software in multiple places
• [ ] along the way, stop using type or command and use findProgram
• [ ] bring back the newPackage options for backwards compatibility, but have them give a deprecation warning.

[d-torrance]

or even provide a function for generating a single cached example, so we can cache only the necessary examples

This would be awesome. I have a pretty hacky function that does this for the Debian package, but a cleaner solution would be great.