Index Nix sources and accept external extraction

[caniko]

Summary

• Add structural Nix extraction to the existing code indexing path.
• Add a format-agnostic --external-extraction envelope for integrations that own their source parsing.
• Preserve normal Graphify building, clustering, incremental replacement, and stale-source pruning for external contributions.
• Keep source-format adapters outside the Graphify repository.

Validation

• 168 detection tests passed.
• 3 external-ingress replacement, validation, and pruning tests passed.
• 8 focused extraction tests passed.
• ruff check passed for the changed Python files.

This PR contains no source-format-specific adapter; integrations provide the generic extraction envelope instead.