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?

Yes, Highlights integrates with Bookends (tutorial here) and Papers (tutorial here).

Is Highlights scriptable?

No, not yet.

Highlights in the Mac App Store

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