I use org-roam and hyperlink to files / folders on disk to make them discoverable like any other thoughts I store in org-roam. Using TRAMP you can even link to

I use org-roam and hyperlink to files / folders on disk to make them discoverable like any other thoughts I store in org-roam. Using TRAMP you can even link to remote files over SSH or other protocols. If you're not an Emacs fan and you din't want to be, Logseq is another tool that looks like it can be used in a similar way.