Added `plyr` dependency back into `compile_download`.  It's the cleanest way I know to deal with variable column numbers. @gavinsimpson if you know a better way that wouldn't use plyr I'm happy to implement it.
Changes to fix class and variable assignments:
- `get_dataset`
  - renamed `site.data` to `site`, making it clear it is part of the `site` class.
  - `dataset` becomes `dataset.meta` since it is one `data.frame` in the `dataset` class.
  - created new `dataset_list` class, similar to the `download_list`.
  - all changes cascaded through the different methods.
Changes to fix class and variable assignments:
- `get_download`
  - the `metadata` object is now properly called `dataset` since it is a `dataset` and is of class `dataset`.
  - `metadata$site.data` is now `dataset$site` to reflect changes to the `dataset` and `site` classes.
  - `submission` has variable names changed.
  - changes cascade throughout methods
  - added a new method for the `dataset_list` class.
Changes to fix class and variable assignments:
- `get_site`
  - mostly changes to the methods for classes.
Fixes reflecting changes to the variable names within classes.  All methods should work now.
Misc. commits.
- Trying to fix a check note about global variables in `compile_list`
- adding new tests to neotoma_test
- cleaning & rebuilding