Provide better examples and documentation for JSON and YAML input

[sobolevnrm]

The JSON documentation exists, it just isn't very good. This section of the manual provides an overview of the keys and values expected in JSON- or YAML-format input. Sorry we don't have more direct examples -- I'll create an issue to generate these in the future.

Originally posted by @sobolevnrm in #256 (comment)

[sobolevnrm]

These examples should include specific invocation instructions per #256 (comment).

[supernova4869]

Have you ever added examples of using json or yaml with APBS to the manual?

[sobolevnrm]

No. However, we welcome community help to improve our documentation. Thank you.

[supernova4869]

Can apbs program directly read yaml file as PBSA calculation input, instead of old plain text format? If so, what is the particular command?

[sobolevnrm]

This is high on my to-do list but I am not sure when I'll be able to get started.