Two options :
1) The sbt dist didn't actually package it. Check the generated zip / tgz, and the generated .jar files to check if it is actually there (it probably is, all under conf/ is packaged normally
2) The cwd is not your project's topdir. You use relative paths, but those only work if the cwd is the project's top level dir. I would use a absolute pathname, where the application's deploy dir is in $HOME, provided by CF.
So, {type = "PEM", path = "conf/certificates/cert.pem"} -> {type = "PEM", path = "${HOME}/conf/certificates/cert.pem" }
Igmar