I do agree with the type of suggestion jcolomb is proposing. I have a lot of projects and I have a lot of common or reference data, common code that is either in .R script that I source, or 1 of two R packages I maintain for myself with code that I like to reuse.
Under projects I would have a group of projects that I maintain through GitHub (which is most of the time), a group of projects, that also unclude 'data projects', that has the common data, and the wee bit of data to coral the data from source and make it usable, and 1 folder 'R', for utils.R that I use to save functions that I make; that if I use often enough, end up in my personal ultils library that is itself a GitHub project.
I do it like this:
/Projects
--> GitHub
--> -->
--> -->
--> --> ...
--> LocalProjects
--> --> /P1_
--> --> /P2_
--> --> /P3_
--> --> ...
--> --> /D1_
--> --> /D2_
--> --> ...
--> --> R
Then basically within each project (P's, D's, and GitHub projects) is structured like this:
/P1_MyExampleProject
--> data
--> figures
--> R
--> reports
--> presentations
--> save
--> scriptsDraft
--> scriptsFinal
and each script in the setup chunk, sets the wd to the root of the project (P1_MyExampleProjec)
Peter