feat: consume .hypatia-baseline.json in governance gate

[hyperpolymath]

Summary

Adds a single, formal exemption convention to the estate governance gate: .hypatia-baseline.json. Same shape as Hypatia findings (severity, rule_module, type, file/file_pattern), so an acknowledged finding can be listed once and silently suppressed by the gate. Companion to hyperpolymath/gitbot-fleet#148.

Why

The language-policy job runs banned_language_file across every caller repo. In-flight migrations (e.g. the ReScript → AffineScript port at gitbot-fleet) keep getting blocked on .res files that are already acknowledged in the repo's baseline. PR authors started inventing alternate ignore conventions (.hypatia-ignore flat-files) to work around the gap. This PR formalises one convention so the estate stops sprouting more.

What

1. validate-baseline job (new) — detects the per-repo baseline file, schema-validates it (ajv when available, jq fallback otherwise), surfaces stale entries (referenced file no longer exists) as warnings. Soft-failure throughout.
2. language-policy job (updated) — is_exempt() now consults .hypatia-baseline.json before falling back to legacy .hypatia-ignore and the inline # hypatia:ignore pragma. The legacy path stays for back-compat; a follow-up PR retires it once the estate has converged.
3. .machine_readable/hypatia-baseline.schema.json — formal JSON Schema (draft 2020-12). Required: severity, rule_module, type, plus exactly one of file / file_pattern. Optional: severity_override, expires_at, note, tracking_issue.
4. scripts/apply-baseline.sh — pure bash+jq filter. Used by the richer findings-list flow this PR seeds; the current workflow integration uses the inline jq lookup instead so the advisory-mode landing has the smallest possible footprint.
5. docs/HYPATIA-BASELINE-FORMAT.adoc — authoritative format doc.
6. docs/EXEMPTION-MECHANISMS.adoc — convention doc: when to use .hypatia-baseline.json vs the estate-wide bot_exclusion_registry.a2ml vs per-PR labels.

Rollout

Advisory mode (default). Exempting a finding via the baseline removes it from the gate output. Blocking-mode promotion (via vars.HYPATIA_BASELINE_MODE = "blocking") is the follow-up after a one-week soak. Documented inline at the top of governance-reusable.yml.

Test plan

• CI green on this branch.
• Manual: caller repo with a baseline file gets a ⏭️ exempt (baseline) line in the language-policy job logs and the gate passes despite the banned file.
• Manual: caller repo without a baseline behaves identically to before (legacy .hypatia-ignore + inline pragma still honoured).
• Manual: caller repo with a malformed baseline gets a validate-baseline warning (not a hard failure during advisory soak).
• Follow-up after one-week soak: flip HYPATIA_BASELINE_MODE to blocking and confirm the gate behaves identically across the estate.

https://claude.ai/code/session_01W3PAoaqgJj3mnM8kjhEqx4

---

Generated by Claude Code

[github-actions]

🔍 Hypatia Security Scan

Findings: 208 issues detected

Severity	Count
🔴 Critical	64
🟠 High	120
🟡 Medium	24

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
    "type": "unpinned_action",
    "file": "governance-reusable.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
    "type": "unpinned_action",
    "file": "governance.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Python file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/a2ml-templates/state-scm-to-v2.py",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/a2ml/bindings/deno/mod.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/lol/test/vitest.config.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/k9-svc/bindings/deno/mod.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "Agda postulate assumes without proof -- potential soundness hole (4 occurrences, CWE-704)",
    "type": "agda_postulate",
    "file": "/home/runner/work/standards/standards/lol/proofs/theories/information_theory.agda",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "critical"
  },
  {
    "reason": "believe_me undermines formal verification (1 occurrences, CWE-704)",
    "type": "believe_me",
    "file": "/home/runner/work/standards/standards/lol/src/abi/Locale.idr",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "critical"
  },
  {
    "reason": "Wildcard CORS -- restrict to specific origins or use env var (1 occurrences, CWE-942)",
    "type": "js_wildcard_cors",
    "file": "/home/runner/work/standards/standards/consent-aware-http/examples/reference-implementations/deno/aibdp_middleware.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  },
  {
    "reason": "innerHTML assignment -- XSS risk, use textContent or SafeDOM (1 occurrences, CWE-79)",
    "type": "js_innerhtml",
    "file": "/home/runner/work/standards/standards/axel-protocol/src/Tea.res.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  }
]

Powered by Hypatia Neurosymbolic CI/CD Intelligence

[github-actions]

🔍 Hypatia Security Scan

Findings: 208 issues detected

Severity	Count
🔴 Critical	64
🟠 High	120
🟡 Medium	24

⚠️ Action Required: Critical security issues found!

View findings

[
  {
    "reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
    "type": "unpinned_action",
    "file": "governance-reusable.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Action hyperpolymath/standards/.github/workflows/governance-reusable.yml@main needs attention",
    "type": "unpinned_action",
    "file": "governance.yml",
    "action": "pin_sha",
    "rule_module": "workflow_audit",
    "severity": "high"
  },
  {
    "reason": "Python file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/a2ml-templates/state-scm-to-v2.py",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/a2ml/bindings/deno/mod.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/lol/test/vitest.config.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "TypeScript file detected -- banned language",
    "type": "banned_language_file",
    "file": "/home/runner/work/standards/standards/k9-svc/bindings/deno/mod.ts",
    "action": "flag",
    "rule_module": "cicd_rules",
    "severity": "critical"
  },
  {
    "reason": "Agda postulate assumes without proof -- potential soundness hole (4 occurrences, CWE-704)",
    "type": "agda_postulate",
    "file": "/home/runner/work/standards/standards/lol/proofs/theories/information_theory.agda",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "critical"
  },
  {
    "reason": "believe_me undermines formal verification (1 occurrences, CWE-704)",
    "type": "believe_me",
    "file": "/home/runner/work/standards/standards/lol/src/abi/Locale.idr",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "critical"
  },
  {
    "reason": "Wildcard CORS -- restrict to specific origins or use env var (1 occurrences, CWE-942)",
    "type": "js_wildcard_cors",
    "file": "/home/runner/work/standards/standards/consent-aware-http/examples/reference-implementations/deno/aibdp_middleware.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  },
  {
    "reason": "innerHTML assignment -- XSS risk, use textContent or SafeDOM (1 occurrences, CWE-79)",
    "type": "js_innerhtml",
    "file": "/home/runner/work/standards/standards/axel-protocol/src/Tea.res.js",
    "action": "flag",
    "rule_module": "code_safety",
    "severity": "high"
  }
]

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