And is also used in my $HOME directory - I like repeating good patterns, or at least well known patterns. (I still have ./etc and ./lib directories in my projects)
I believe with direnv or a similar tool (e.g. Emacs’s directory-local feature) one can append $REPO/.config to XDG_CONFIG_HOME, $REPO/.local/bin to PATH and so on so that when in the context of a particular directory everything Just Works.
I think all this agentic stuff could live quite happily in $REPO/.config/agents/.