an ecosystem of tools > a second brain
Our thoughts are scattered, nonlinear, complicated. Sometimes we feel the thought before it actually makes sense. Tasks are often rigid structures. Notes and ideas are often not. To combine them into one interface seems counter-intuitive. Ideally we might be able to link between them, hence one-stop solution like org-mode. However alluring this may be, you’re still more or less tied to Emacs to get most of the benefit and ecosystem.
The fix is to not have a rigid workflow for a fluid process—thinking. Use the best tool for the job, however you feel like it. Often, these tools come as standards and specifications, like RSS, Atom, vTODO, Markdown, OPDS, EPUBs, and your browser (all those pending tabs and bookmarks are also dangling information). There is absolutely no single tool to integrate it all, without losing functionality, portability, spontaneity. Put things down where it is easiest, and move them where they’re most accessible later.
To find things from different places, use APIs to pull them in one place, and use tools like fzf, fd, rg, zk, your editor, etc. to pull things together.