A feature I have been waiting for in every research management software I’ve tried is a mapping feature that helps you visualize how tags connect. For example if I tag a document with “leadership, medicine, faculty development” and a second document with “medicine, education, motivation, faculty development” and a third with “leadership, motivation, training” it would visually show me the connections between the articles and allow me to click on the connecting lines to see which articles have both leadership and motivation or both medicine and faculty development. This is a difficult concept to explain in words, I hope this makes sense!
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Just a suggestion, but have you looked at Mohiomap? It might not do exactly what you want, but will allow you to visualize the connections that you define between files on your drives.
As for Paperpile a Tag Cloud would be a very helpful feature for consideration in the future. However, integrate MetaPDF and give us a word connector first pretty-please.