I/O Refactoring

[andrewfullard]

:pencil: Description

Type: :roller_coaster: infrastructure

This PR refactors the I/O part of TARDIS to split it up better by category e.g. Composition (and its parts).

Also fixes bug with CSVY dimensions

Fixes #2582

:vertical_traffic_light: Testing

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[andrewfullard]

What really needs to happen to resolve the CSVY bug (and may happen in this PR?) is to remove all loc[1:] calls across the I/O part of the code and take stock of how we really want to read in tables of densities, mass fractions, etc

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[andrewfullard]

@jvshields pluralized instances of mass_fraction in this PR. The Composition class still has lots of singular form.