I print them out and put them in piles. I write on them with pens.

Obsidian with the new canvas feature is awesome. ResearchRabbit and Elicit have been useful too

Overleaf

My annotations make too little sense for anything but me to possibly understand them :)

I save them as pdfs and write notes in the margins.

I write crimson notes on my cave wall.

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Thank you for this! Excellent suggestions.

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I do the same if the file is not so voluminous. I prefer taking notes with pen rather doing it digitally. Maybe I'm old soul :)