FEAT: rename files to reflect equations

[aaronjridley]

Is your feature request related to a problem? Please describe.
It is hard to figure out which files contain which codes. Have to use grep a LOT to figure this out.

Describe the solution you'd like
We don't really want every function to have it's own file, since there will then be thousands of files. One solution could be that we have a naming convection for the different files, such as [neutral]/[ion]_equation_term.cpp. For example neutral_momentum_ion_drag.cpp.

There are a LOT of files that are more general, so we would have to come up with a naming standard for those, too.

Describe alternatives you've considered
Keep going the way that we are and maybe have a map of the code.

Additional context
grep, grep, grep, grep, grep. too many grep.