I can’t use -v because this container will be used as a build step in a CI/CD pipeline and as I understand it, it is just run as is.
Using -v to expose your current directory is the only way to make that .deploy/mup.js file inside your container, unless you are baking it into the image itself using a COPY directive in your Dockerfile.
Using the -v option to map a host directory might look something like this:
docker run \
-v $PWD/.deploy:/data/.deploy \
-w /data \
docker-mup deploy --config .deploy/mup.js
This would map (using -v ...) the $PWD/.deploy directory onto /data/.deploy in your container, set the current working directory to /data (using -w ...), and then run deploy --config .deploy/mup.js.