When running the dokku command in a directory that the dokku user does not have access to - such as /root - popd will fail loudly (starting in Ubuntu 16.04). This change ignores those errors and changes the working dir in the bin to /tmp.
Refs #5012
We should treat the project.toml as an optional file, as is the Procfile. Additionally, moving the file into place early will ensure there is no chance of selecting the wrong file.