How do you handle the last modified case?

Denote does not insert any meta data or heading pertaining to edits in the file. I am of the view that these either do not scale well or are not descriptive enough. Suppose you use a “lastmod” heading with a timestamp: which lines where edited and what did the change amount to?

This is where an external program can be helpful. Use a Version Control System, such as Git, to keep track of all your notes. Every time you add a new file, record the addition. Same for post-creation edits. Your VCS will let you review the history of those changes. For instance, Emacs’ built-in version control framework has a command that produces a log of changes for the current file: ‘M-x vc-print-log’, bound to ‘C-x v l’ by default. From there one can access the corresponding diff output (use ‘M-x describe-mode’ (‘C-h m’) in an unfamiliar buffer to learn more about it). With Git in particular, Emacs users have the option of the all-round excellent ‘magit’ package.

In short: let Denote (or equivalent) create notes and link between them, the file manager organise and provide access to files, search programs deal with searching and narrowing, and version control software handle the tracking of changes.