fix(ci): adopt the template's inline hypatia-scan.yml

.github/workflows/actions.lock

@@ -42,7 +42,11 @@ workflows:
     '.github/workflows/guix-policy.yml':
         - 'actions/checkout@v7.0.1'
     '.github/workflows/hypatia-scan.yml':
-        - 'metadatastician/standards@46ee18323305d5b36e2eef936e47dd54c39ea736'
+        - 'actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9'
+        - 'actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1'
+        - 'actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9'
+        - 'erlef/setup-beam@54075bcc5e249e4758d363f27d099f55d843f124'
+        - 'github/codeql-action@9b3254085494b55a0f7c4c2b3d2d52cc712ce370'
     '.github/workflows/label-triage.yml': []
     '.github/workflows/labels.yml': []
     '.github/workflows/lock-sync-gate.yml': []

.github/workflows/hypatia-scan.yml

@@ -1,35 +1,170 @@
 # This workflow is managed by gh actions-lock.
 # SPDX-License-Identifier: MPL-2.0
 #
-# Standalone Hypatia security scan (push / PR / weekly). This is NOT a duplicate
-# of the `hypatia-scan` job in `static-analysis-gate.yml`: that job exists to
-# feed the gitbot-fleet LEARNING pipeline (via `deposit-findings`), whereas this
-# workflow is the repo's independent security scan. Same tool, two consumers.
-# See .github/workflows/README.adoc.
+# Self-contained Hypatia neurosymbolic security scan + SARIF upload (`category:
+# hypatia`) satisfying the `Hypatia` code-scanning tool requirement in the
+# `Base` branch ruleset on `main`, as well as push, weekly schedule, and manual
+# dispatch runs.
+#
+# This is the ONLY workflow that runs Hypatia (static-analysis-gate.yml used to
+# run it a second time at the same pin, with a second cache, its own duplicate
+# "fail on critical" gate and a differently-shaped output). See the header of
+# fork-governance.yml for the layering.
+#
+# Two outputs matter downstream:
+#   * the SARIF, for code scanning;
+#   * `hypatia-findings.relativized.json` in the `hypatia-scan-findings`
+#     artifact, which the Fork governance verdict grid reads. The artifact name
+#     matches hypatia-scan-reusable.yml's, so adopting that reusable later needs
+#     no change in fork-governance.yml.
+#
+# `name:` is a cross-workflow EDGE: verdict-grid-publish.yml names "Hypatia
+# Security Scan" in its `workflow_run.workflows`. Renaming this workflow without
+# renaming it there silently stops the grid re-rendering;
+# scripts/check-workflow-edges.sh fails the CICD Squabbler gate when the two
+# disagree.
 name: Hypatia Security Scan
 
 on:
+  pull_request:
   push:
     branches: [main, master, develop]
-  pull_request:
-    branches: [main, master]
   schedule:
     - cron: '0 0 * * 0'
   workflow_dispatch:
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
+
 permissions:
-  actions: read      # required by the reusable workflow (staleness check reads workflow runs)
   contents: read
-  security-events: write
 
 jobs:
   hypatia:
-    uses: metadatastician/standards/.github/workflows/hypatia-scan-reusable.yml@46ee18323305d5b36e2eef936e47dd54c39ea736
-    with:
-      # The scanner the verdict grid names (fork-governance.yml and
-      # verdict-grid-publish.yml, --hypatia-ref). Without it the reusable runs
-      # its own default (adb2f41 at 46ee183), not the commit the grid claims.
-      hypatia-ref: be98f74ce93df200752f3798efa1305bfa3e0e10
+    name: Hypatia Neurosymbolic Analysis
+    runs-on: ubuntu-24.04
+    timeout-minutes: 20
+    permissions:
+      contents: read
+      security-events: write
+      vulnerability-alerts: read # Dependabot alerts, for Hypatia's DA rules
+    env:
+      HYPATIA_SHA: 'be98f74ce93df200752f3798efa1305bfa3e0e10'
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
+          persist-credentials: false
+
+      - name: Setup Elixir 1.19.4 / OTP 28.5.0.8 for Hypatia scanner
+        uses: erlef/setup-beam@54075bcc5e249e4758d363f27d099f55d843f124 # v1.24.1
+        with:
+          elixir-version: '1.19.4'
+          otp-version: '28.5.0.8'
+
+      - name: Cache pinned Hypatia build
+        id: cache-hypatia
+        uses: actions/cache@55cc8345863c7cc4c66a329aec7e433d2d1c52a9 # v6.1.0
+        with:
+          path: |
+            ~/hypatia
+            ~/.hex
+            ~/.mix
+          key: hypatia-sarif-${{ runner.os }}-otp28.5.0.8-elx1194-${{ env.HYPATIA_SHA }}
+
+      - name: Build pinned Hypatia scanner
+        run: |
+          set -euo pipefail
+          if [ ! -x "$HOME/hypatia/hypatia" ] || [ ! -x "$HOME/hypatia/hypatia-cli.sh" ]; then
+            rm -rf "$HOME/hypatia"
+            git init "$HOME/hypatia"
+            git -C "$HOME/hypatia" remote add origin https://github.com/hyperpolymath/hypatia.git
+            git -C "$HOME/hypatia" fetch --depth=1 origin "$HYPATIA_SHA"
+            git -C "$HOME/hypatia" checkout --detach FETCH_HEAD
+            (
+              cd "$HOME/hypatia"
+              mix local.hex --force
+              mix local.rebar --force
+              mix deps.get
+              MIX_NO_PUBSUB=1 mix escript.build
+            )
+            chmod +x "$HOME/hypatia/hypatia" "$HOME/hypatia/hypatia-cli.sh"
+          fi
+
+      - name: Run Hypatia JSON and SARIF analysis
+        id: scan
+        env:
+          # The API-backed rules (code-scanning, Dependabot, secret-scanning,
+          # branch-protection, baseline-health) return no findings without a
+          # token. Scoped to this step. The job token reaches code-scanning
+          # (security-events) and Dependabot (vulnerability-alerts) alerts;
+          # it cannot read secret-scanning alerts, which need an App or PAT.
+          GITHUB_TOKEN: ${{ github.token }}
+        run: |
+          set -euo pipefail
+          HYPATIA_FORMAT=json "$HOME/hypatia/hypatia-cli.sh" scan . --exit-zero > hypatia-findings.json
+          jq -e 'type == "array"' hypatia-findings.json >/dev/null
+
+          HYPATIA_FORMAT=sarif "$HOME/hypatia/hypatia-cli.sh" scan . --exit-zero > hypatia.sarif
+          jq -e '.runs | type == "array" and length > 0' hypatia.sarif >/dev/null
+
+          # Repo-relative paths, because the verdict grid's delta column compares
+          # findings against `git diff --name-only`, which is repo-relative: an
+          # absolute path would never match, and every finding would be counted
+          # as "standing" instead of "in this change".
+          jq --arg ws "$GITHUB_WORKSPACE/" '
+            map(if (.file | type) == "string" then
+                  .file |= (if startswith($ws) then .[($ws | length):] else . end)
+                else . end)' hypatia-findings.json > hypatia-findings.relativized.json
+
+          CRITICAL="$(jq '[.[] | select(.severity == "critical")] | length' hypatia-findings.json)"
+          HIGH="$(jq '[.[] | select(.severity == "high")] | length' hypatia-findings.json)"
+          TOTAL="$(jq 'length' hypatia-findings.json)"
+          {
+            echo "critical=$CRITICAL"
+            echo "high=$HIGH"
+            echo "total=$TOTAL"
+          } >> "$GITHUB_OUTPUT"
+
+      # Evidence for the verdict grid. Uploaded even when the scan step failed:
+      # a missing artifact and a failed scan are different facts, and the grid
+      # can only say "orange" for the first. `if-no-files-found: warn` because a
+      # scan that never produced a file is already visible as a red step here.
+      - name: Upload Hypatia findings for the verdict grid
+        if: ${{ always() }}
+        uses: actions/upload-artifact@cf430e030ddbb5b0abf93d22962f4752f3646cd9 # v7.0.2
+        with:
+          name: hypatia-scan-findings
+          path: |
+            hypatia-findings.json
+            hypatia-findings.relativized.json
+          if-no-files-found: warn
+          retention-days: 90
+
+      - name: Upload Hypatia SARIF to GitHub Code Scanning
+        if: github.event_name != 'pull_request' || github.event.pull_request.head.repo.full_name == github.repository
+        uses: github/codeql-action/upload-sarif@9b3254085494b55a0f7c4c2b3d2d52cc712ce370 # v4.39.1
+        with:
+          sarif_file: hypatia.sarif
+          category: hypatia
+
+      - name: Enforce zero critical Hypatia findings
+        env:
+          CRITICAL_COUNT: ${{ steps.scan.outputs.critical }}
+          HIGH_COUNT: ${{ steps.scan.outputs.high }}
+          TOTAL_COUNT: ${{ steps.scan.outputs.total }}
+        run: |
+          set -euo pipefail
+          {
+            echo "## Hypatia Neurosymbolic Scan"
+            echo ""
+            echo "- Critical: ${CRITICAL_COUNT}"
+            echo "- High: ${HIGH_COUNT}"
+            echo "- Total findings: ${TOTAL_COUNT}"
+          } >> "$GITHUB_STEP_SUMMARY"
+          if [ "$CRITICAL_COUNT" != "0" ]; then
+            echo "::error::Hypatia reported ${CRITICAL_COUNT} critical finding(s)"
+            exit 1
+          fi