If you’re hitting the same issue I’ve been hitting, I think this needs a new version on your end. To check, add a folder to a repo locally, then try running pijul record twice. The second one shouldn’t do anything, but for me, on alpha 48, it does.
This also happened in a very early version of pijul. I thought, this was a feature, so you don’t have to put empty hidden files into a directory, which is meant to be empty, like in git.
What we ran into isn’t that “directories are tracked independently of their contents”, it’s that “the initial record of a directory, regardless of whether it contains anything, is a file, which leads to an immediate dirty repo state requiring a second record to convert the file to a directory”.