Flatten the directory structure

All data is kept in the data directory. Functions are kept in the
functions directory. But now all the scripts are kept in the root
directory.
Use .R instead of .r

Rake gets confused by .Rout and .r and so rebuilds everything all the
time, which is decidedly undesirable.
Use Rake, not Make

Because even though Make has a more concise rule syntax (come on,
Rake!), Make sucks compared to Rake and the power of Ruby.
Added Catholic Diocese data