refactor(indexer): Rework config and cli arguments

[tomxey]

Description of change

This patch reworks a number of the indexer configs and cli arguments to try and centralize where the configuration for the indexer is loaded. This also cleans up the cli arguments into well defined subcommands instead of using boolean flags for deciding if a jsonrpc or indexer writer service should be started.

The old CLI is still kept for backward compatibility with an intention to remove it in the future.

Links to any relevant issues

fixes: #6201

Type of change

Rafactoring

How the change has been tested

The tests are still failing, patch is WIP
cargo ci-clippy
cargo test --profile simulator --package iota-indexer --test rpc-tests --all-features

Change checklist

Tick the boxes that are relevant to your changes, and delete any items that are not.

• I have followed the contribution guidelines for this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have added tests that prove my fix is effective or that my feature works
• I have checked that new and existing unit tests pass locally with my changes

Release Notes

• Protocol:
• Nodes (Validators and Full nodes):
• Indexer:
• JSON-RPC:
• GraphQL:
• CLI:
• Rust SDK:
• REST API:

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