Consistent file naming convention

[KCGallagher]

Maybe we say that files which run analysis are prefaced with 'main' in the main directory, or stored as notebooks in the examples directory? All other files in the main directory define functions etc to solve the system? (Or should these be in a separate directory themselves?)

Let me know your thoughts so we can organise something consistent!

[KCGallagher]

This is as uniform as we will realistically make this, given the limited scope of this project, and reliance on the current file structure in saving routines