Put CWDs and directories of create files in config

[Right now](https://github.com/ViDA-NYU/reprozip/blob/986e807ef5947745aa030dcb13f06c414770d863/reprozip/reprozip/pack.py#L199-L204) the packer reads the directories that are used as working directory by a process or in which files are created, and adds them (without their contents) to the archive.

This is certainly a good idea but there is no reason these don't appear in the configuration file (other than them being directories and not files). They should probably appear there, so the packer doesn't have to load in the trace database at all.