*On that note, I hope future versions of MarginNote will have real-time database updates so that restarting the app isn’t necessary to view newly created files. The process of “clipping” (saving) the webpage to the directory is quick, but it does often require opening MarginNote multiple times in order for the PDF to be inserted into MarginNote’s SQLite database and listed in MarginNote’s file browser.* Unless you need to take notes on webpages whose dynamic content (like JavaScript) is critical to the notes themselves (which I think is unlikely), it should work for 99% of note-taking use cases. webarchive, the extension leverages Apple’s WebKit rendering engine, which I have found to be surprisingly faithful to original webpage renders.
Something I do that (kind of) acts like a web-clipper with MarginNote is by saving PDF webpages to a subdirectory in /Library/Containers/QReader.MarginStudyMac/Data/Documents/ using DEVONthink’s browser extension.
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