Fix reference links on civic-scraper docs

[zstumgoren]

Reference links for the civic-scraper docs appear to have been lost in the conversion from standard rst to markdown. Need to figure out fix (appears to use CommonMark Spec via myst python library.

[zstumgoren]

Here's a problem example of the problem from the Usage page, where [Command line] and [Custom scripts] should be clickable links.

[zstumgoren]

Solution requires updating cross-references to targets. For example: [Command line] -> [Command line](cli) where (cli)= has been defined as a target elsewhere in the document.