[Core] Make viper great again

[Olshansk]

Objective

Cleanup, improve and clarify how viper work and is used throughout the codebase.

Origin Document

It started in #902 with this comment:

Then it crossed over in #891 with this comment

Goals

• Clearer separation between CLI and API code
• Parsing the config consistently in all CLI commands.
• Handling flags consistently in all commands.

Deliverable

• Refactor how viper is used to make it clear and understandable
• Update the documentation for how & why we use viper in a certain way

Non-goals / Non-deliverables

• Removing viper as a dependency

General issue deliverables

• Update the appropriate CHANGELOG(s)
• Update any relevant local/global README(s)
• Update relevant source code tree explanations
• Add or update any relevant or supporting mermaid diagrams

Testing Methodology

• Task specific tests or benchmarks: make ...
• New tests or benchmarks: make ...
• All tests: make test_all
• LocalNet: verify a LocalNet is still functioning correctly by following the instructions at docs/development/README.md
• k8s LocalNet: verify a k8s LocalNet is still functioning correctly by following the instructions here

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Creator: @Olshansk
Co-Owners: @bryanchriswhite