As a workaround you could rename your .env file to something else and mount it as .env in the docker-compose volume options.
The workaround that I've found for this problem is to set "AUTOENV_ENV_FILENAME=.env.user" and then inside the project folder, I'm now using ".env.user" instead of just ".env".
I'll use this hack until Docker guys fix Docker Compose.
function lenv {
if [ -f '.env' ]; then
source .env
fi
}
function cd { builtin cd $@; lenv; }Rename .env to something else and reconfigure autoenv.