Are you using Ulysses exclusively for all your writing and research materials? That looks interesting. My research is currently all over the place, OmniFocus, Notes and my Bibliography Management System. I really need to look into alternatives.

@jl_siewert this is what was / ia happening to me stuff everywhere , I’ve a lot of folders as well if stuff that I lose track so am trying to claw it back into Ulysses and Papers. I am going to try and use the Ulysess attachments feature to drop in images of onenote notes and photos of things I scribble on paper and even photos of real book pages. I’m also clawing stuff into an etherpad but I think I’m going to copy that into Ulysses now and then edit there. I’ll probably try and start to build my DeckSets inside that Ulysses group as well now.

Our university licensed Citavi as a reference tool. It can hold and organize PDFs, quotes and ideas. Unfortunately it's Windows only. Also it only really integrates with Word or TeX. Not really ideal, but at least it's the same software my colleagues use.

@jl_siewert ours went for EndNote can’t stand it was a fan of Papers and bite the bullet and returned to the ReadCube version

I really liked the trial of Bookends but there is just to much collaboration going on that it would be worth it to use a completely separate tool.

I have Parallels running most of the time anyway (and a ridiculous amount of RAM).