Earlier quoted context omitted.
I was also unhappy with how reference managers handle annotations. So I rolled my own app ( https://getcahier.com ), with highlight management integrated in the application. This enables me to extract highlights according to topics, organize them in notes using document elements (like collapsible notes and outlines) and use them to plan more complex arguments. This makes it much easier to read actively. On the paper…
Cahier looks great! Any plans to add backup/sync? Also, is the data store encrypted at rest even when the app is actively being used?
The data is all local, so there's no need for encryption yet. But when we implement sync it'll be end to end encrypted.