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refactor: deep audit — fix stale naming, add innervation architecture
Phase 1 housekeeping: - Replace all stale -scm naming with -a2ml across 33 satellite A2ML files (agentic, playbook, neurosym, anchor, meta, overlay) - Update TOPOLOGY.md: fix diagram, add protocol + integration layers, honest 80% overall (was false 100%) - Rewrite ROADMAP.adoc: reflect actual state, add Phase A (innervation), Phase B (evidence), Phase C (visibility), Phase D (maturity) - Wire Justfile: test/build/lint/fmt/clean now run real sub-project suites instead of stubs; add crg-grade and crg-badge recipes - Fix REQUIRED-FILES.md URLs (×2) New artefacts: - coordination.k9: nerve receptor declaring invariants, protected paths, afferent/efferent/reflex innervation signals - .verisimdb/config.toml: port 8097, 5 octad schemas (crg-grade, proof-status, compliance-scan, ecosystem-link, inline-annotation) - .github/workflows/hypatia-scan.yml: dogfooding self-scan - component-readiness-grades/SELF-ASSESSMENT.adoc: grade B with evidence inventory and documented gaps to A Architecture decision: begin transition from 6a2 static files to innervation model (coordination.k9 + VeriSimDB + Hypatia + inline annotations). Standards repo is the pilot. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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‎.github/workflows/hypatia-scan.yml‎

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# SPDX-License-Identifier: PMPL-1.0-or-later
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# Hypatia Neurosymbolic CI/CD Security Scan — SELF-SCAN (dogfooding)
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# The standards repo that defines Hypatia scans itself with Hypatia.
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name: Hypatia Self-Scan
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on:
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push:
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branches: [ main ]
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pull_request:
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branches: [ main ]
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schedule:
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- cron: '0 0 * * 0' # Weekly on Sunday
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workflow_dispatch:
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permissions: read-all
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jobs:
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scan:
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name: Hypatia Neurosymbolic Analysis (Dogfooding)
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runs-on: ubuntu-latest
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steps:
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- name: Checkout repository
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uses: actions/checkout@34e114876b0b11c390a56381ad16ebd13914f8d5 # v4
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with:
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fetch-depth: 0
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- name: Setup Elixir for Hypatia scanner
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uses: erlef/setup-beam@2f0cc07b4b9bea248ae098aba9e1a8a1de5ec24c # v1.18.2
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with:
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elixir-version: '1.19.4'
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otp-version: '28.3'
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- name: Clone Hypatia
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run: |
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git clone --depth 1 https://github.com/hyperpolymath/hypatia.git "$HOME/hypatia"
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- name: Build Hypatia scanner
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working-directory: ${{ env.HOME }}/hypatia
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run: |
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if [ ! -f hypatia-v2 ]; then
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cd scanner && mix deps.get && mix escript.build && mv hypatia ../hypatia-v2
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fi
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- name: Run Hypatia scan
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id: scan
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run: |
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echo "Scanning standards repo (dogfooding)"
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HYPATIA_FORMAT=json "$HOME/hypatia/hypatia-cli.sh" scan . > hypatia-findings.json
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FINDING_COUNT=$(jq '. | length' hypatia-findings.json 2>/dev/null || echo 0)
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CRITICAL=$(jq '[.[] | select(.severity == "critical")] | length' hypatia-findings.json 2>/dev/null || echo 0)
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HIGH=$(jq '[.[] | select(.severity == "high")] | length' hypatia-findings.json 2>/dev/null || echo 0)
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MEDIUM=$(jq '[.[] | select(.severity == "medium")] | length' hypatia-findings.json 2>/dev/null || echo 0)
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echo "findings_count=$FINDING_COUNT" >> $GITHUB_OUTPUT
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echo "critical=$CRITICAL" >> $GITHUB_OUTPUT
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echo "high=$HIGH" >> $GITHUB_OUTPUT
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echo "medium=$MEDIUM" >> $GITHUB_OUTPUT
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echo "## Hypatia Self-Scan Results (Dogfooding)" >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "The standards repo scans itself. Findings here are compliance" >> $GITHUB_STEP_SUMMARY
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echo "gaps between what we define and what we practice." >> $GITHUB_STEP_SUMMARY
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echo "" >> $GITHUB_STEP_SUMMARY
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echo "| Severity | Count |" >> $GITHUB_STEP_SUMMARY
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echo "|----------|-------|" >> $GITHUB_STEP_SUMMARY
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echo "| Critical | $CRITICAL |" >> $GITHUB_STEP_SUMMARY
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echo "| High | $HIGH |" >> $GITHUB_STEP_SUMMARY
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echo "| Medium | $MEDIUM |" >> $GITHUB_STEP_SUMMARY
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echo "| **Total**| $FINDING_COUNT |" >> $GITHUB_STEP_SUMMARY
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- name: Run panic-attack assail
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run: |
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# Install panic-attack if available
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if command -v panic-attack >/dev/null 2>&1; then
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panic-attack assail . > panic-attack-findings.json 2>&1 || true
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echo "panic-attack scan complete"
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else
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echo "panic-attack not available in CI — install from hyperpolymath/panic-attacker"
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echo "[]" > panic-attack-findings.json
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fi
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- name: Upload findings artifacts
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uses: actions/upload-artifact@65c79d7f54e76e4e3c7a8f34db0f4ac8b515c478 # v4
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with:
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name: standards-self-scan
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path: |
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hypatia-findings.json
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panic-attack-findings.json
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retention-days: 90
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- name: Check for critical issues
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if: steps.scan.outputs.critical > 0
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run: |
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echo "Critical self-scan issues found in the standards repo!"
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echo "The repo that defines standards has compliance gaps."
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echo "Review hypatia-findings.json for details."
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# Warn but don't fail — fix forward

‎.meta/REQUIRED-FILES.md‎

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- [RSR (Rhodium Standard Repositories)](https://github.com/hyperpolymath/rhodium-standard-repositories)
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- [Mustfile Specification](https://github.com/hyperpolymath/mustfile)
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- [SCM Format Family](https://github.com/hyperpolymath/meta-scm)
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- [A2ML Format Family](https://github.com/hyperpolymath/standards/tree/main/meta-a2ml)

‎.verisimdb/config.toml‎

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# SPDX-License-Identifier: PMPL-1.0-or-later
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# VeriSimDB instance configuration for the standards monorepo
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# See: https://github.com/hyperpolymath/verisimdb
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[instance]
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name = "standards"
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port = 8097
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volume = "standards-verisimdb-data"
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base_image = "cgr.dev/chainguard/wolfi-base:latest"
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[instance.health]
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endpoint = "/health"
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interval_seconds = 30
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# ─────────────────────────────────────────────────────────────
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# Octad Schemas — what this instance stores
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# ─────────────────────────────────────────────────────────────
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# CRG grade tracking — component readiness grades with evidence
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[[octad_schema]]
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entity = "crg-grade"
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description = "Component Readiness Grade assessment with evidence chain"
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[octad_schema.modalities]
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semantic = ["component", "grade", "evidence_summary", "reviewer", "repo"]
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temporal = ["graded_at", "promoted_from", "next_review"]
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provenance = ["graded_by", "basis_commit", "ci_run_id", "methodology"]
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vector = ["component_embedding"]
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# Proof status — formal verification evidence
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[[octad_schema]]
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entity = "proof-status"
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description = "Formal proof verification result from ECHIDNA"
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[octad_schema.modalities]
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semantic = ["file_path", "prover", "theorem_name", "axioms_used", "trust_level"]
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temporal = ["verified_at", "last_source_changed", "proof_age_days"]
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provenance = ["echidna_version", "backend", "ci_run_id"]
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document = ["proof_term_cbor", "type_signature"]
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# Compliance scan results — Hypatia findings
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[[octad_schema]]
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entity = "compliance-scan"
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description = "Hypatia/panic-attack scan finding"
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[octad_schema.modalities]
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semantic = ["repo", "finding_type", "severity", "rule_id", "message"]
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temporal = ["scanned_at", "resolved_at", "age_days"]
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provenance = ["scanner", "scanner_version", "recipe_applied"]
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graph = ["related_repos", "caused_by_commit"]
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# Ecosystem relationships — derived from actual imports/usage
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[[octad_schema]]
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entity = "ecosystem-link"
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description = "Relationship between repos/components derived from code"
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[octad_schema.modalities]
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semantic = ["source_repo", "target_repo", "link_type", "strength"]
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temporal = ["first_seen", "last_confirmed", "stale_after_days"]
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graph = ["dependency_chain", "transitive_consumers"]
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provenance = ["detection_method", "evidence_file", "evidence_line"]
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# Inline annotations — @trust/@contract/@grade from code
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[[octad_schema]]
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entity = "inline-annotation"
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description = "Machine-readable annotation extracted from source code"
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[octad_schema.modalities]
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semantic = ["file_path", "line", "annotation_type", "value", "function_name"]
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temporal = ["extracted_at", "source_last_modified"]
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provenance = ["commit_sha", "extractor_version"]
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vector = ["function_embedding"]
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# ─────────────────────────────────────────────────────────────
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# Groove Integration
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# ─────────────────────────────────────────────────────────────
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[groove]
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enabled = true
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service_name = "standards-verisimdb"
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capabilities = ["octad-store", "vql-query", "annotation-index"]
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[groove.signals]
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# Afferent: what this instance emits
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emit = [
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"crg.grade.changed",
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"proof.verified",
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"proof.stale",
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"compliance.finding.new",
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"compliance.finding.resolved",
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"ecosystem.link.discovered",
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"ecosystem.link.stale",
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"annotation.extracted",
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]
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# Efferent: what this instance responds to
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respond_to = [
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"commit.pushed", # re-index annotations
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"ci.completed", # ingest scan results
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"echidna.proof.verified", # store proof certificate
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"hypatia.scan.completed", # store findings
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]

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