thx all for this thread!
it is enlightening, and a breeze. also thx for – in the course of it – asking that interesting notetaking question (– see also Favorite External Editors for Notes in macOS & iOS) … and pointing to Keypoints!
it is good to know; and certainly the question of exegesis vs. topology (and other fundamental aspects of excertping and annotation) is a central one for (post-)humanities. as btw is the inherent question of excerpting vs annotation that is itself another complexion to streamline…
– I have also found over the years that folding the whole research system into one-or-two apps doesn´t work (as good as e.g. DT is), as one always ‘bends’ an application agst its architecture – and it´s just a permanent uphill-struggle agst affordance/habit/flow to do that. (so I am still struggling to make DT a really useful app for visual / image research (the ‘other’ form of information), which just behaves differently than text-centric research…)
for this reason I for myself arrived at MarginNote (currently MarginNote3 for excerpting PDF (and other material as websites!). it not only allows different views of notes, tagging them, filtering them according to metadata and other clue systems – but also brings a full-blown mind-mapping solution along with it (actually one that can keep up with all the pro-apps, which I do not list here!). – this mindmap has different rather sensational aspects to it – besides giving a visual rendering and backtracking to the linear exceprts/annotations: (a) it can itself be manipulated (sorting, moving, linking, further annotations that write back to the ‘PDF notes’!, etc.) (b) it can be exported as interactive pdf, going out alongside the notes/excerpts (besides all the options to export single notes, note sets with backlinks etc.) (c ) different excerpt-maps can be combined, manipulated and searched as topological/conceptual maps (search generally is another strongpoint of MN).
there are some weaknesses/drawbacks of course: PDFs have to ‘live’ in MN; the UI needs some getting used too (it´s the kind of you either love or hate it; or just get along…); and (like with Keypoints and others) it neccessitates a rather elaborate personal workflow/protocol to keep things in sync with whatever the personal system in DT is.
– anyway I thought I drop a mention of it, as it relates to several of the mentioned aspects/questions in this thread (including the OPs question).
best, oliver