allow file dependencies to live in folders

[daviddalpiaz]

Allow "main" folder to utilize sub-directories such as data or img.

[coatless]

Good catch! Though, in the future, we probably want to migrate to an R analysis project structure. (e.g. restricting to pulling files from data/ and images/ and so on.

[daviddalpiaz]

My hubris has come back to bite me. Didn't thoroughly test. Files are being copied, but not into folders like img. Will see if I can fix later, but at a quick glance, the solution isn't clear to me.