Refactor & tidy

[dfalster]

Reorganise files, functions and tests

• seperate update_taxonomy into component functions
• move code for taxon splitting into update_taxonomy
• expand testing (#118), reorganise tests to be more intuitive
• move some functions into their own seperate files
• remove temporary variables
• simplify update_taxonomy where possible
• renamed variables:
  • taxonomic_reference -> taxonomic_dataset
  • variables ending _clean -> _align (#128)

Fixes #129, Fixes #101, Fixes #128 Fixes #106 Fixes #135

Contributes to #120 #127 #110 #118