After extensive search and evaluation for a decent replacement of Ecco Pro I finally wrote a tool myself many years ago which helped me to keep track of all my projects since then: https://github.com/rochus-keller/crossline/
Contextualise excels at organising information-heavy projects and activities consisting of unstructured and widely diverse data and information resources.
I just use a plain git repository with markdown files, structured hierarchically. Total freedom of how to organize things, and I can work with the tools I like (git/terminal text editor).
I honestly tried most of the note taking apps, none really worked out for me, I always end up using my memory directly, with a mix of few large txt files synced in my drive.
https://github.com/cu/silicon