Rename file (.r -> .R) for case-sensitive filesystems (e.g. Linux extN).
Remove dependence on the authors' directory structure

(N.B. this requires the program to be run from the unpacked top directory)
Include directories required for the script to generate output

(Git does not support empty directories in the repository, so we need
a README file.)
Add brief instructions about how to run the system

Signed-off-by: Keith Winstein <keithw@mit.edu>