On recommendation of several people, I decided to try the annotation app, Highlights. Although I was intrigued with several of the features, after extensive use, I can’t recommend the app. The program still needs work before I could reliably use it in my writing workflow.I found two of Highlights features especially attractive:

The ability to extract each highlight or comment as its own markdown file.
The ability to underline references in the PDF and have those references automatically appended/linked to extracted notes.

I trialed Highlights for about a week. Ultimately, even with the intriguing features, The appnwas far too buggy for me to adopt.Here are some of the issues I faced:

References would not reliably link to a note. I could find no rhyme or reason for this behavior. Sometimes the feature worked, sometimes it didn’t. No matter what I tried, I was unable to remedy this issue. My attempt at editing markdown files led to frustration—my edits were often erased.
Even when the reference extraction worked, there is a bug that alters the markdown file, adding additional markdown to each reference. With many references, this bug makes each file unreadable.
I found no way to configure the order, type, and appearance of the metadata.
Extraction of figures from the manuscript were buggy and unreliable.
Metadata was impossible to change. Initially, I set Up the app to automatically retrieve metadata. Unfortunately, several of the paPers the software Retrieved had erroneous metadata. Once imported, I found the metadata impossible to change. Since I add the title, author, And other metadata to every one of my extracted notes, this was The fatal flaw that caused me to end my trial.

Although I am intrigued by several of the features of the Highlights App, I will continue to use my tried and true method of note extraction using Skim. I plan keeping an eye peeled for these issues to be fixed within Highlights. With some improvements, I could see the app becoming my Mac PDF reader of choice.