Push the TOML configuration as default

[azerupi]

As part of #275 we would like to push the TOML configuration as the default and deprecate the JSON config. We are not going to remove the JSON config just yet, but we are going to show a deprecation warning.

Here are some the things that need to happen:

• Parity between the JSON config and TOML config
• Move and rename dest, src and theme_path to

  source = "path/to/sources"
  
  [output.html]
  destination = "path/to/output"
  theme = "path/to/directory"

• Add a key for an additional custom stylesheet Add CSS without overriding theme #266 Add an empty, but included last, custom.css file #178

  [output.html]
  additional-css = ["path/to/file.css"]

• Add tests for each config key
• Reading the config should not overwrite unspecified keys some values are overwritten by read_config #240
• Document the TOML config