Command line arguments are out of date with respect to latest Pandoc versions

[nealkruis]

For example, we now get a warning every time pandiff is executed:

[WARNING] Deprecated: --atx-headers. Use --markdown-headings=atx instead.

It might also be nice to pass all arguments and their values straight through to Pandoc so the CLI doesn't have to try to keep up with changes in the Pandoc CLI?