Yes, go to Preferences –> Markdown and turn on “Use # for title/author headers”
Yes, go to Preferences –> PDF and set what color you want for each type of annotation.
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.
No, not yet.
This happens when the PDF is exported from Skim as it saves a backup of the highlighted text in the comment-field of the annotation.
Yes, if you select the text containing the DOI-link and selecting “Lookup metadata” in the View-menu (Cmd+Alt+R) Highlights will use the selection for fetching metadata.
Please email me with as much information as you can provide on when/how/why it crashed (crash reports and screenshots are very helpful).
Yes, you can download it here. The demo has the same features as the full version, but only extracts annotations from every other page of the PDF.
Yes, Highlights uses standard embedded annotations which are supported by most PDF readers on both OS X and iOS.
Some PDF apps (including Skim) and most reference managers use non-standard annotations which are not compatible with Highlights. However, most of these apps allow you to export the PDFs with embedded annotations which will work in Highlights.
Under Customize in Preferences, you can set which information should be included in each annotation (including author, modification date and color category).
Check out this tutorial.
Color coding allows for categories of annotations sorted by color. By going to Preferences –> Colors you can see the current order in which the colors will be sorted. You can reorder the sorting and rename the each color to represent a category.