{
  "generated_at": "2026-09-23T16:50:19+00:00",
  "command": "python -m msr_pipeline analyze",
  "seed": 580,
  "gitskills_db": "agent_skills_sample.db",
  "gitskills_db_sha256_from_manifest": "683888c923a51952fb66f83f21351ed5bf1127ddddf380e517592ae27c367658",
  "rules_file": "skill_risk_rules.yaml",
  "rules_file_sha256": "111aa8f78af22e8274f047106dcd27c18ca4f735c1669fba4775b8dbc84efab5",
  "rules_active": 19,
  "high_risk_severity_cutoff": 6,
  "main_similarity_threshold": 0.5,
  "row_counts": {
    "occurrences": 29786,
    "representatives": 13000,
    "main_population": 12965,
    "script_files_scanned": 5153,
    "lineage_pairs_at_lowest_threshold": 332
  },
  "versions": {
    "python": "3.12.10",
    "pandas": "3.0.5",
    "numpy": "2.5.3",
    "scipy": "1.18.1",
    "statsmodels": "0.15.0",
    "matplotlib": "3.11.2",
    "pyyaml": "6.0.3"
  },
  "outputs": [
    "population_flow.csv",
    "rq1_prevalence_by_rule.csv",
    "rq1_prevalence_by_category.csv",
    "rq2_reach_summary.csv",
    "rq2_mannwhitney.csv",
    "rq2_bootstrap.csv",
    "rq2_negbin.csv",
    "rq2_category_tests.csv",
    "rq3_threshold_sweep.csv",
    "rq3_summary.csv",
    "rq3_lineage_pairs.csv",
    "rq3_differing_pairs.csv",
    "scripts_summary.csv",
    "sensitivity_summary.csv",
    "rq1_prevalence_by_category.png",
    "rq2_copies_by_group.png",
    "rq3_threshold_sweep.png"
  ],
  "runtime_seconds": 100.5
}