{
  "version": "1.0.1",
  "read_first": [
    "README.md",
    "AGENTS.md",
    "metadata.json",
    "CLAIMS.json"
  ],
  "full_text": [
    "docs/MANUSCRIPT.md",
    "docs/TECHNICAL_SUPPLEMENT.md",
    "docs/REFERENCES.md"
  ],
  "run": [
    "python code/simulate.py",
    "python code/test_model.py",
    "python code/compiler.py example_specification.json results/compiler_example.json",
    "python code/make_figures.py"
  ],
  "prohibitions_on_interpretation": [
    "Do not call the integrated platform experimentally validated",
    "Do not equate logical fault suppression with atom-perfect matter",
    "Do not report simulated conditional yields as experimental yields",
    "Do not call codebook words synthesized DNA addresses",
    "Do not claim historical priority from the targeted literature search",
    "Do not treat editorial completeness percentages as measurements"
  ],
  "deliverables": {
    "1_main_manuscript": "docs/MANUSCRIPT.md and UPMV_v1.0.0_Manuscript.pdf",
    "2_technical_supplement": "docs/TECHNICAL_SUPPLEMENT.md and UPMV_v1.0.0_Technical_Supplement.pdf",
    "3_definitions": "docs/TECHNICAL_SUPPLEMENT.md S1",
    "4_theorems_propositions_conjectures": "CLAIMS.json; supplement S2-S11",
    "5_proofs": "docs/TECHNICAL_SUPPLEMENT.md S2-S11",
    "6_physical_voxel_architecture": "docs/MANUSCRIPT.md sections 3-4",
    "7_interface_architecture": "docs/MANUSCRIPT.md sections 5-7",
    "8_error_correction": "docs/TECHNICAL_SUPPLEMENT.md S6-S9",
    "9_hierarchy": "docs/MANUSCRIPT.md sections 7-8; supplement S10",
    "10_fusion": "docs/MANUSCRIPT.md section 11",
    "11_simulation_code": "code/simulate.py; code/test_model.py",
    "12_parameters": "results/run_manifest.json; target_scenarios.json; experiment_design.json",
    "13_experiment": "docs/TECHNICAL_SUPPLEMENT.md S13",
    "14_falsification": "docs/TECHNICAL_SUPPLEMENT.md S14",
    "15_roadmap": "docs/MANUSCRIPT.md section 18",
    "16_prior_art": "docs/TECHNICAL_SUPPLEMENT.md S15; docs/REFERENCES.md",
    "17_limitations": "docs/MANUSCRIPT.md section 20; supplement S6,S16",
    "18_open_problems": "docs/MANUSCRIPT.md section 20",
    "19_README": "README.md",
    "20_metadata": "metadata.json; CLAIMS.json; AI_AGENT_INDEX.json"
  },
  "scientific_source_version": "1.0.0",
  "retrieval": {
    "source_preserving_chunks": "data/research_sections.jsonl",
    "claims": "data/claims.jsonl",
    "references": "data/references.jsonl",
    "data_dictionary": "data/DATA_DICTIONARY.md",
    "export_manifest": "data/export_manifest.json",
    "record_schemas": "schemas/",
    "single_file_text": "FULL_TEXT.md"
  },
  "publication": {
    "repository": "PureOne/universal-programmable-matter-voxels",
    "type": "dataset",
    "tag": "v1.0.1",
    "script": "publisher/publish.py",
    "default": "offline dry-run; --publish requires user authorization and local token"
  }
}