Initial Commit.

Removes the variables section from config.R and puts it into its own
files. Long files are bad and config.R was getting a little long.
Updates to packages and variables files.
Changes to file format.
Changes to file format.
Changes to file format.
Changes to file format.
File format change.
Changes to file format.
Changes to file documentation.
Changes Documentation to Man.

Bringing format into line with R package specs.
Changes to file contents.
Adds branches and cleans things up.
Small change to documentation.
Sets this file up. I think this will make everything easier to manage.
Major improvements to the project template layout.

Someday, I need to stop changing this.

- Replaces config.R with packages.R and variables.R.
- Deleted the SQL and graphics folders and their associated README
- files. Not all analyses are going to have these folders, so I don't
- think it should be a default part of the template.

* R/config.R: