feat(graph-layers) Reorder layout APIs ahead of internal helpers

[ibgreen]

Summary

• move protected updateGraph implementations below the public APIs in legacy layouts to keep internal helpers separate
• shift internal helpers like _engageWorker, _generateSimulator, and _strength after the public surface across D3/d3-force/GPU/experimental layouts
• clean up minor style issues such as default node-position fallbacks and comment alignment while keeping behavior intact

Testing

• yarn lint
• yarn vitest run --project node modules/graph-layers/test/core/graph-engine.spec.ts modules/graph-layers/test/core/graph-layout.spec.ts modules/graph-layers/test/layouts/d3-dag-layout.spec.ts

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Codex Task