Node relationships, backwards or forward?
A one-to-many relationship (also in DB design) is typically created by referencing the parent from the child. In the Jobs/Job Applications case, this translates into a reference from Job Application to Job, not vice versa.

In the Project/File case, if each file can only belong to one project, then it's also a one-to-many relationship and so File should reference Project. This is definitely how it should be if we were designing database tables for those entities.

However, in terms of Drupal and node references and given this particular example, Files are almost like properties to the Project node. So I wouldn't be surprised to see Files referenced from Project in a multiple-value node reference field, just for convenience.