What will break if I point :source-paths to ["."]? I'd like to keep source code in a top-level directory named after the namespace, not tucked inside src/clj.

Answering myself: figwheel broke horribly 😃

Is it possible to specify the credentials directly in project.clj when using https://github.com/s3-wagon-private/s3-wagon-private ?

yes.

:plugins [[s3-wagon-private "1.1.2"]]
  :repositories [["s3" {:url ""
                        :username :env/aws_access_key
                        :passphrase :env/aws_secret_key}]]

replace the :env/aws_access_key and :env/aws_secret_key with strings containing your credentials