Lots of small updates based around avoiding data.set

- Updated a handful of tests to remove depricated methods.
- Replaced the extraction method used by eml_get(eml, "data.frame").
The new approach is built more around functions than S4 methods.
Most importantly, it handles the type casting of columns more
explicitly, which requires comparing different parts of the metadata
(e.g. dateTime@formatString, not only ratio vs interval but integer
vs numeric, etc.)
- Updated the top-level interface to support col.defs and unit.defs all
  the way down.