ux: re-consider user experience when running multiple configurations against same inputs

[jdhoffa]

          > I still feel some tension about the config that I can't quite explain. I guess our cookbook suggests that one might/should run parts of the process multiple times with tweaked settings, which implies to me that they may be using multiple config files and have multiple roughly equivalent sub directories, e.g. `analyse_by_group` and `analyse_by_sector`. And we even facilitated using full paths to each directory, so those sub directories don't even need to be in the same project directory (iirc we specifically thought that the `input` directory might likely be in a separate location).

I don't have a good suggestion here (sorry), just being forward about a bit of hesitation I have.

Originally posted by @cjyetman in #258 (comment)

[jdhoffa]

When one fininshes a run, and then wants to go back and run another analysis:

• I will need to go back and change the config.yml values
• I will also need to change the directory names

Maybe we can make it more clear that if you want to adjust the configuration, you also need to update the output directory names so that you don't overwrite data.