[tconfrey]

Scaling your system is always going to be a problem, no matter what tools you use.

I hear you on isearching. To support multiple files you could look at ag.el for fast cross-file search (although not incremental like isearch).

Alternately you can use :tags: to add a different dimension of information by which things can be grouped. org-agenda can then be used to see items by tag (also since they are just text you can search them in a buffer). I use org-agenda in 'F'ollow mode whereby a second buffer shows the selected agenda item in its original context. It helps visualize where things are while navigating.

The new hotness, ala org-roam, is bidirectional linking with tiny files. That would probably be a pain to migrate to, and isn't really aligned with your free-form model. But it might be the way to scale over the long term.

[sfink]

That sounds promising. You understood perfectly where I am and what I'm looking for, thanks.

I'll check out ag.el. The incremental search is not that big a deal, I'm usually searching for a keyword anyway.

I looked briefly at org-roam, and I agree with your assessment. It looks like it adds friction to the part that needs to be as smooth as possible for me: adding notes. I could probably dummy something up for searching by making a command that shells out to grep or whatever, but that feels like fighting against the data model.