Slightly tangential, but Markdown does actually "kinda" support comments with a little bit of abuse of the link syntax. Almost every renderer will swallow the comment in the following example:
> This is a quote of some kind
[//]: # (This won't be in the rendered output.)
Blah blah blah
Keypoints brings a lot of other things to the table than just comments, including an upcoming possibility of crosslinking between PDF docs [0], but I've wanted to add annotations often enough to small Markdown documents enough that I've memorised the above little trick. It even works with the original Markdown.pl implementation.
I am interested to see how this compares to https://highlightsapp.net/ but it looks neat, especially if it starts at a place of integration with other platforms.
Keypoints is similar to Highlights App in that it extracts your PDF highlights into Markdown. That said, there are more differences between those two apps than similarities. I've outlined the major differences at [0].
Most importantly, Keypoints stores each highlight as an individual (Multi)Markdown note, so you can filter/gather them freely and independent of its source context. However, each note is self-contained and keeps its context (i.e. to which PDF / publication it belongs), and selecting a note opens again the exact PDF location containing the original highlight annotation.
Each highlight note can have metadata (like tags, labels or citekeys) that can be clicked to filter by these elements. You can cross-link your notes (incl. link types [1]) and your network of notes gets dynamically visualized (the graph can also be used for navigation).
In addition, Keypoints parses recognized elements from the plaintext notes and exposes them as data model properties via scripting (see an example: [2]). This will allow for fine-grained integrations with other apps.
Thx for the reminder! But the edit option is no longer in the page, probably cuz I've already edited it multiple times. I'll pay attention to this the next time. Anyway, we have the real author in this thread Lol
In the distant future, I hope to also develop a version for iOS. But for now, due to this being a part-time effort, I have to focus on a single platform. I've also outlined some of my reasonings here: https://forum.obsidian.md/t/markdown-layer-on-top-of-pdf/122...
If you don't mind an Electron or web-based app with a subscription, you could also look at Zenreader [0], Polar [1] or maybe even Readwise [2]. Zotero will also have a PDF Reader app with Markdown export soon [3]. And some cross-platform note taking / PKM apps also have some kind of PDF annotation support (directly: Logseq [4]; via plugins: Obsidian [5], Roam Research [6]).
That said, all these offerings are very different from each other so you'd have to look closely what fits best.
[0] https://keypoints.app/forums/viewtopic.php?f=2&p=788