are you allergic to the quote functionality? (bottom right)
also - I think the UX of digital devices often doesn't compare with pen and paper. It adds layers of interaction that don't always add proportionate value.
I think using a computer as an extension of your memory is always going to be dependent on your search capability, naming conventions and organisational skills. Its not always an improvement.
One tool I've used to some success is google docs. The functionality on it's own is pretty spartan, but there are many homebrew add-ons you can download that allow you to bend the platform to your needs.
The add-on in particular I've found invaluable is "Table of Contents" by LumApps.
It does exactly what you think it would- creates a sidebar with a table of contents of hyperlinks that take you to each "chapter" defined by you.
My system for organizing this is naming each "chapter" as the date it was entered and a one or two word description of what the entry contains. This allows for fast navigation and an "at a glance" view of all my notes. Plus you can access it anywhere you can find an internet signal!
I'm not actually sure if the add-on works on mobile devices, but definitely any browser.
I did not read the thread.
I also take an large amount of notes. I normally mark the date on each page and when I re-read my notes and integrate the notes in the rule books, I add a mark to indicate that those notes has been reread and integrated in the rule book (or discarded) so no need to re-read it.
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"relied too much on memory"
yea that's always a bad thing, the whole point, or one key point of a computer is that it's an extension of our memory
so we can focus on more important things