add documentation about where paper can be, and how to tell whedon

[danielskatz]

1. We should add something to https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain that suggests where to put the paper's source

2. If this is not in the repo root or a paper directory in the master brand, whedon can be told where to find it in some cases. It would be nice if this was a variable that could be specified at submit time. and changed later by whedon, so that whedon's generate pdf would be able to use this variable.