Are you using flakes? I think this is a flakes specific thing.

Well, it doesn't silently ignore files, it tells you if the work tree is dirty.

Though I've tripped over the different behaviors of the repl vs the rest of the tools myself in funny ways

Get in the habit of running jj desc midway through a commit. Have you just discovered an insight in an old module? Do you see how you will write the next few hunks of code? Did you have a moment of clarity where you zoomed out and saw what the next week will look like? Document it! Let your commit messages have multiple paragraphs, each written at a different time. Fill your commits with annotations about what you were doing so that future-you will understand past-you.

The reasoning here is that, aside from the jj file subcommands which directly alter the index, almost any jj subcommand will work. You might as well pick a subcommand which advances your goals.

Never seen this behavior. Since when is nix tied to git? Are you using lix or something?