I often kept a personal "notes" file while I was working on a project/feature. I now think that what I should have done is check that file into the source tree, at the top level directory for whatever feature I was doing.

I like the "check it into the tree" instinct. I've tried tracking observations and lessons in README files across a monorepo, but I felt they went stale almost immediately. Maybe your more focused files would work better. But checked in or not: have you found yourself reopening those earlier notes when you start the next feature? Or do they mostly just sit there?