Major rewrite.

- Removes all references to TemplateR.
- Improves the instructions for new users.
- Generally makes things sound / read better.
- Adds a section specifically to discuss files, not just the folders.
Removes an unnecessary blank line.
Better to set these on by default.
Make it more like a R package.

I am still learning about R packages, but I think it makes sense to
make this structure RESEMBLE an R package more than make it resemble
something I conjure up out of thin air. To that end, I renamed some of
the folders to align them with the defaults in a R Package. It is
better form, makes it easier to use for experienced package
developers, etc.
* R/README.md: