I keep projects in a directory of their own. So I end up with project/src as the "main" repo, project/src-$variant for related repos or worktrees and project/build* for build trees. As such, I have .mrconfig files with entries like:

[project/src]
checkout = git clone github:org/project src

However, when doing mr checkout, I first need to mkdir project. Can intermediate directories be made? There are some other oddities around (such as that src bit) and upon a (successful) checkout, my post_checkout cwd seems to be off as well:

fatal: not a git repository (or any parent up to mount point /)
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set).