After using Bear.app and Things.app for a while, I've moved firmly in the file over app camp. Apps can be enjoyable to use until you don't have access to the app anymore (platform, longevity,...). Now I'm using Emacs with org files, but could just as well use any tools that favors files. Any novel use case I want, I can script it out in a moment, while still enjoying the benefits of viewing my information on most platforms.

> Something I have been wondering about is the "backlink" feature. It would be cool to link items/notes together through references. What I would be looking for is a Unix tools that can scan my text files for references to other files in the hierarchy

The only thing you need is some kind of structure, like the wiki link format or org link format, and you could 'rgrep' the notes directory for a particular link (vim and emacs can put the result in a buffer).