Refactor of package code

[MJHutchinson]

Currently, the code in the mapping and cleaning packages is intimately tied to the specific data we have. This will need to be cleanly separated for use to a) do the simulation tests and b) release the code for general use.

The main suggestion would be to depreciate the use of environments in package functions and have them take explicit arguments instead. The use of environments can still remain in our loading code, but using them as function arguments make code very opaque and unclear what a function needs in the env to work.