apollo_config: make native the sole config-load path

[nimrod-starkware]

Delete the preset branch of load_and_process_config so load_native is the only
loader: remove the ConfigFormat enum + --config_format arg, the per-param CLI
override parser (build_args_parser/update_config_map_by_command_args), the
load-time config_schema.json read, the pointer-resolution and #is_none-folding
functions (split_pointers_map, split_values_and_types,
update_config_map_by_pointers, update_optional_values), and the config_parity
dev bin. Callers stop passing --config_format. Pointer/#is_none DEFINITIONS,
CONFIG_POINTERS, dump()/SerializeConfig, and CONFIG_SCHEMA_PATH are retained for
later phases.

Co-Authored-By: Claude Opus 4.8 (1M context) noreply@anthropic.com

[reviewable-StarkWare]

This change is 

[nimrod-starkware]

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• apollo_deployments: delete Rust component-config topology mirror #14688
• apollo_deployments,apollo_integration_tests: source harness component configs from jsonnet #14687
• deployment: drop redundant YAML sequencerConfig; source port-uniqueness from jsonnet #14659
• apollo_config,workspace: remove SerializeConfig trait and preset-dump machinery #14654
• apollo_config,apollo_node_config,apollo_config_manager: rework get_config_presentation off dump() #14653
• apollo_node_config,apollo_node: delete CONFIG_POINTERS data and pointer-remap from secrets bin #14652
• apollo_node_config,apollo_config_manager,apollo_integration_tests: retire preset config-generation path #14651
• apollo_node_config,apollo_deployments: assert cross-component equality for formerly-pointer-resolved fields #14650
• apollo_deployments: delete base app_configs and the preset-parity test machinery #14649
• apollo_node_config,apollo_node,deployment: source private_parameters from secrets schema, drop value config schema #14648
• apollo_deployments: retire dead preset/replacer generation machinery #14647
• deployment,apollo_deployments: drop config_format plumbing and retire preset config path #14646
• deployment: add native config layers for the testing overlays #14645
• deployment: add dummy_for_testing native config override layer #14632
• apollo_config: make native the sole config-load path #14631 👈 (View in Graphite)
• apollo_config,apollo_node_config: make config fields with custom deserializers serialize symmetrically #14630
• apollo_integration_tests,apollo_node_config: load integration-test node config via native format #14629
• apollo_deployments: expose jsonnet build() evaluator behind a testing feature #14686
• deployment: extract base-layer start-block numbers into shared constants #14685
• deployment: add mainnet native config override layer #14628
• deployment: add sepolia-alpha native config override layer #14627
• apollo_deployments: test overrides list match #14626
• deployment: add sepolia-integration native config override (chain_params + replacers) #14674
• deployment: add native node-config builder and wire it into the ConfigMap #14609 : 1 other dependent PR (#14655 )
• deployment: thread config_format from CLI to node container arg #14608
• apollo_deployments,deployment: set storage-reader-server ports as constants #14607
• apollo_node: add new CLI arg to parse config #14606
• apollo_deployments: check applicative config matches deployed app_configs #14489 : 2 other dependent PRs (#14480 , #14505 )
• apollo_deployments: assemble and deserialize node config from jsonnet #14487
• apollo_deployments: assemble full node config via build.libsonnet #14486
• apollo_deployments: distributed layout jsonnet test #14485
• apollo_deployments: consolidated layout jsonnet test #14484
• apollo_deployments: test hybrid layout for infra config #14483
• apollo_deployments: introduce hybrid layout for infra config #14482
• apollo_deployments: introduce jsonnet building blocks for infra config #14481
• apollo_deployments: jsonnet applicative config #14479
• main

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PR Summary

High Risk
This is a breaking change to how every binary loads configuration (arity, file shape, and no CLI/env overrides), so mis-deployed or legacy launch flags will fail at startup until callers are updated.

Overview
Config loading is now native-only: nested base JSON plus a flat dotted-key secrets file (exactly two --config_file paths). The preset pipeline, ConfigFormat / --config_format, per-parameter CLI and env overrides, and runtime pointer / #is_none resolution at load time are removed.

load_and_process_config no longer reads config_schema.json; clap only registers --config_file. SequencerNodeConfig::load_and_process passes CLI args straight into that loader. Docs and tests use the two-file native flow; integration node spawns drop --config_format. The config_parity dev binary is deleted. Dumping (SerializeConfig, CONFIG_POINTERS, preset artifacts) stays for deployment tooling.

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