LayerStructure updates for abiotic_simple

[davidorme]

Description

This PR introduces changes to make the abiotic_simple model work with the new LayerStructure in #421.

@vgro - if you can have a look at the changes to see if anything looks mad (but the tests pass, so hopefully not) then I can merge it down into #421.

The main changes to the actual code are passing LayerStructure down the chain rather than layer_roles and then using that functionality.

Fixes #446

Type of change

• New feature (non-breaking change which adds functionality)
• Optimization (back-end change that speeds up the code)
• Bug fix (non-breaking change which fixes an issue)

Key checklist

• Make sure you've run the pre-commit checks: $ pre-commit run -a
• All tests pass: $ poetry run pytest

Further checks

• Code is commented, particularly in hard-to-understand areas
• Tests added that prove fix is effective or that feature works

[vgro]

@davidorme thanks for your help with this, it looks really good, a few minor tweaks. I'll finish the hydrology stuff that I started yesterday and then I'll make the changes here, I'll let you know when I need you to review again.

[davidorme]

The abiotic_simple tests all pass locally, which is the point of this subbranch, so merging it down into #421.