[FEATURE] Refactor FS Structure

[sondavidb]

Description

The current code structure is confusing and is largely inherited from stargz, which in turn attempts to mimic containerd ideas. Due to fundamental differences between SOCI and stargz, we should heavily look into how we structure our codebase to be more clearly aligned with how we want to structure SOCI.

This would avoid problems outlined in various PRs, most recently #849, which mutates multiple function headers to pass a FSConfig all the way down to the layer level, not to mention the many paths it could have taken to get there when it should all be relatively streamlined. If we had clearer abstractions and better mechanisms, it could be a trivial change.

This PR is largely meant to track our plans for design structure for this project going forward.

Describe the solution you'd like

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Describe any alternative solutions/features you've considered

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Any additional context or information about the feature request

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