A lot of my notes and tasks wind up having bits of code and sometimes large data files associated with them, so I've landed on a similar path of using plain text/org mode files, but aided by a little shell function `today` that creates-if-not-exists a new subdirectory named for the date whenever I use it:

    function today() {
        TODAY_DIR="$HOME/today/"
        DATE_DIR=$(date +'%Y-%m-%d')


        if [ ! -d  $TODAY_DIR$DATE_DIR ];
        then
            mkdir -p $TODAY_DIR$DATE_DIR
        fi;

        echo $TODAY_DIR$DATE_DIR
    }

So I just do something like `emacs $(today)/tasks.org`. Easy to grep across time, copy things forward (I guess I could do with having `yesterday` and `tomorrow` as well). It's really nice to just use basic CLI tools and little scripts to manage notes and todo lists. Project specific stuff gets a subfolder name every day so it's easy enough to glob ~/today/*/{project}/....

It's a sort of landing zone for all of the miscellaneous artifacts I might deal with on a given day as well:, e.g. `wget -P $(today) https://site.net/cooldata.gzip`.