I want atx-header style Markdown headers, is this possible?
Yes, go to Preferences –> Markdown and turn on “Use # for title/author headers”
Can I have a standard color for each type of annotation?
Yes, go to Preferences –> PDF and set what color you want for each type of annotation.
Is there tagging support in Highlights?
Yes, Highlights supports per file tagging. Select a color for Tags in Preferences –> PDF –> “Underlining power tools”. Underline the words or short sentences in the PDF you want to use as a tag with the selected color. Tags will be embedded as PDF keywords and exported as Finder-tags when saving.
In addition, Highlights supports per annotation tags “Split files” is enabled in Preferences –> Export. To use this feature as add tags as comments to the annotation using the syntax @tagname e.g. @important or @review. The tags will be added as Finder-tags to the file representing that annotation when exporting as split HTML/Markdown files or to DEVONthink.
Does Highlights integrate with any reference managers?
Is Highlights scriptable?
No, not yet.