Well, the best way to explain is to take the excellent example of Bear (Writer)’s Safari extension, which clips the web page or else selected text and copies it (in Markdown) to a Bear note. You’re more than half way there, at a guess. Similar extensions exist for OneNote and DEVONthink, and of course you can use sharing services to copy pages or bits thereof – or in some cases, just links – to any number of other apps (Together, Keep It, Curiota, EagleFiler, Yojimbo, DEVONthink etc. etc. etc.). But the good thing about a Safari extension is that it keeps Agenda to the forefront of your users’ minds, as it were (“top of mind” thing), and of course you can devise a suitably attractive icon.
The Bear extension is the most directly comparable; I had the strong impression you’d already been inspired by Bear (re: typography, elegant formatting tools etc.) in any case, but perhaps I’m wrong? I suspect there’s Markdown happening under the skin in Agenda, hence your copying/pasting options. If you haven’t installed Bear already, I’d strongly advise it. It might also give you some ideas about the use of tags (as would Quiver, actually) as an alternative organisational option in the left-hand navigation bar…
Keep up the good work!