Track Graphify Nix integration

[caniko]

This issue carries forward the Nix integration scope from superseded PR #1787. The implementation was split into smaller reviewable PRs; use this issue for the remaining integration decisions and completion tracking.

Scope

• #1995 — Add reproducible Nix packaging and CI
  • uv2nix flake
  • package, app, devShell, and hermetic pytest outputs
  • simit-generated CI and pre-commit wiring
• #1996 — Add Graphify NixOS module and PostgreSQL extraction
  • Graphify NixOS service module
  • PostgreSQL extraction integration
  • separation of servers and extraction jobs
• #1998 — Index Nix sources and accept external extraction
  • structural Nix extraction in the existing code-indexing path
  • format-agnostic --external-extraction ingress for integrations that own source parsing
  • preserve Graphify building, clustering, incremental replacement, and stale-source pruning for external contributions
  • source-format adapters remain outside this repository

Completion criteria

• Nix package and module interfaces are agreed and documented.
• Nix CI remains reproducible and validates the supported outputs.
• NixOS service behavior and extraction-job lifecycle are documented.
• The replacement PRs are merged or explicitly closed with the reason recorded here.
• README/install guidance points users to the supported Nix path.

Related

• Superseded implementation history: #1787
• Related but separate provider transport work: #1999 — Route semantic extraction through generic ACP

Do not add new implementation commits to #1787; use the replacement PRs above and update this issue as the integration lands.