BIG (project-wide) update: Set project's home directory, using environment variable (set by user independently/externally, usually in .bashrc file), instead of getwd(). This initially was designed to be used one time/place throughout the project (.Rprofile), but due to issues with knitr's handling working directory, in order to support running R modules (and reports) independently from each other, I have to make this change project-wide.