Bundle: specify which directories/files to include/ignore

I'm doing a biomedical research project, and I have a directory structure that looks like this:

project
- cache
- manuscript
- plots
- presentations
- scripts
- tables

I want to make my research code more easy to share, so I used packrat. It works great.
However when I bundle my project, it includes all directories, including cache and intermediairy objects. Some of these files are actually generated by the script, so they don't have to be included; others (such as presentations) aren't relevant to share but handy to have in the same folder.

Would it be possible to specify which directories/files to ignore during the bundling?

I thought of creating a separate .Rproject in the scripts directory, but now I invoke all scripts using scripts/file.R so that would cripple those files.

For now I think I'll have to change the tar manually.

Start by tracing the bundle operation for a project containing directories such as cache, manuscript, plots, presentations, scripts, and tables. Review how a .Rproject and paths such as scripts/file.R are handled; done means users can specify files or directories to include or ignore without breaking existing script invocation.