When setting the `--app` flag, there was a special case for the config plugin. This plugin used to take the `--no-restart` flag as the first argument - and still did until this change - resulting in an invalid call to the plugin subcommands. What is worse is that this functionality carried over to all other plugins as they were rewritten in golang, and thus the issue spread without us knowing.
The fix is to support GNU flag parsing rules, which Golang does not do by default (Because Of Reasons™). Switching to `github.com/spf13/pflag` fixes this issue, and also allows positional arguments to be placed wherever, even in the middle of flags.
Closes#4255
Rather than attempting to always extract the Procfile, reference the one that was extracted by the last deploy. This fixes issues where 'docker container cp' may fail intermittently for lord knows what reason.
Closes#4083
