fix(schema): v0.6.2 — move Drug/FAQ injection to wpseo_schema_graph; fix peptide 500

Root cause: inject_graph_pieces() added plain PHP arrays to wpseo_schema_graph_pieces.
Yoast Schema_Generator::filter_graph_pieces_to_generate() calls get_class() +
is_needed() on every piece expecting Abstract_Schema_Piece objects — a plain array
produces: PHP Fatal: get_class(): Argument #1 ($object) must be of type object,
array given. All peptide monograph pages returned HTTP 500; non-peptide pages were
unaffected (is_singular guard).

Fix: remove wpseo_schema_graph_pieces hook entirely. New inject_graph_nodes() method
hooks wpseo_schema_graph at priority 12 (after enrich_webpage_piece at 11), which
receives the fully-assembled graph as array-of-arrays — safe for plain array appends.

Also adds regression test (test-jsonld-peptide-piece.php) that:
- Reproduces the v0.6.1 get_class(array) TypeError (fails-before)
- Confirms inject_graph_nodes Drug+FAQ emission is correct (passes-after)

Agent-Session: jsonld-peptide-piece-fix v0.6.2

.github/workflows/cto-review.yml

@@ -1,20 +1,17 @@
 name: CTO Review
 
-# Automated PR review powered by Claude + DeepSeek + Kimi (via OpenRouter)
+# Automated PR review powered by Claude Haiku (via OpenRouter).
-# plus Neurometric PR-Summarizer (a Qwen3-4B task-specialist SLM).
 #
-# During the A/B window (until further notice), every PR gets reviewed by FOUR models
+# A/B panel decision 2026-06-12: panel dropped to Haiku-only.
-# in parallel. The PR comment shows each model's verdict side-by-side so we can compare
+# Evidence: convo/cto/threads/2026-06-qa-ab-review/02-analyst-findings.md
-# quality/cost on real PRs before picking a permanent default.
+# DeepSeek: high false-positive rate (absint()="code exec", PLUGIN_DIR="dir traversal").
+# Kimi: ~60% model failure rate across 13 PRs sampled.
+# Neurometric: summarizer only, zero unique-real findings, unreliable heuristic verdict.
+# Haiku: 0 failures, lowest noise, equivalent real-signal catch rate vs 4-voice panel.
 #
-# Neurometric is a "prose voice": it does not support OpenAI tool-calling, so its
+# Does NOT merge. Posts formal APPROVE/REQUEST_CHANGES/COMMENT reviews.
-# contribution is raw markdown + a heuristic verdict. It is never the primary voice.
 #
-# Does NOT merge. Does NOT post formal APPROVE/REQUEST_CHANGES reviews — always COMMENT
+# Requires repo secret: OPENROUTER_API_KEY
-# (GITHUB_TOKEN can't formally approve PRs without repo-setting toggle).
-#
-# Requires repo secrets: OPENROUTER_API_KEY, NEUROMETRIC_API_KEY (optional; the
-# Neurometric voice self-skips with an inline error note if the key is missing).
 #
 # Cost cap: tracked in Repository Variables (CTO_REVIEW_SPEND_CENTS, CTO_REVIEW_CAP_CENTS).
 # Default cap is 1000 cents ($10/month). Auto-resets on the 1st of each month.
@@ -123,17 +120,18 @@ jobs:
           git fetch origin ${{ github.event.pull_request.base.ref }} --depth=50
           BASE_SHA="${{ github.event.pull_request.base.sha }}"
           HEAD_SHA="${{ github.event.pull_request.head.sha }}"
-          DIFF=$(git diff --no-color "$BASE_SHA" "$HEAD_SHA" | head -c 400000)
+          # Write the diff to a file, not a step output / env var. Passing a
+          # ~400KB diff through the process env (execve argv+envp) exceeds the
+          # runner ARG_MAX and fails the next step with "Argument list too long".
+          # File transport also sidesteps the ~1MB step-output cap.
+          git diff --no-color "$BASE_SHA" "$HEAD_SHA" | head -c 400000 > /tmp/cto-review-diff.txt
           FILES=$(git diff --name-only "$BASE_SHA" "$HEAD_SHA")
-          SIZE=$(echo -n "$DIFF" | wc -c)
+          SIZE=$(wc -c < /tmp/cto-review-diff.txt)
           {
             echo "size=$SIZE"
             echo "files<<EOF_FILES"
             echo "$FILES"
             echo "EOF_FILES"
-            echo "diff<<EOF_DIFF"
-            echo "$DIFF"
-            echo "EOF_DIFF"
           } >> "$GITHUB_OUTPUT"
 
       - name: Load repo conventions
@@ -150,18 +148,17 @@ jobs:
             echo "EOF_CONV"
           } >> "$GITHUB_OUTPUT"
 
-      - name: Call 4 models in parallel (OpenRouter + Neurometric)
+      - name: Call Haiku via OpenRouter
         if: steps.budget.outputs.skip != 'true'
         id: review
         env:
           OPENROUTER_API_KEY: ${{ secrets.OPENROUTER_API_KEY }}
-          NEUROMETRIC_API_KEY: ${{ secrets.NEUROMETRIC_API_KEY }}
           PR_TITLE: ${{ github.event.pull_request.title }}
           PR_BODY: ${{ github.event.pull_request.body }}
           PR_AUTHOR: ${{ github.event.pull_request.user.login }}
           PR_NUMBER: ${{ github.event.pull_request.number }}
           REPO_NAME: ${{ github.event.repository.name }}
-          DIFF: ${{ steps.diff.outputs.diff }}
+          DIFF_PATH: /tmp/cto-review-diff.txt
           DIFF_SIZE: ${{ steps.diff.outputs.size }}
           CHANGED_FILES: ${{ steps.diff.outputs.files }}
           CONVENTIONS: ${{ steps.conventions.outputs.content }}
@@ -183,24 +180,17 @@ jobs:
           fi
 
           python3 - <<'PY'
-          import json, os, sys, urllib.request, concurrent.futures
+          import json, os, sys, urllib.request
 
           api_key = os.environ["OPENROUTER_API_KEY"]
 
-          # A/B harness: four models. Each gets the same prompt.
+          # Haiku-only reviewer. A/B panel dropped 2026-06-12 per QA data:
-          # Primary model's verdict drives the heading. Others are labeled.
+          # DeepSeek high false-positive rate, Kimi ~60% failure rate,
-          # Edit this list to change the roster (or drop to 1 after A/B window closes).
+          # Neurometric zero unique-real findings. Haiku retained as sole voice.
-          #
+          MODEL_SLUG = "anthropic/claude-haiku-4.5"
-          # provider_type semantics:
+          MODEL_DISPLAY = "Claude Haiku 4.5"
-          #   - "openrouter_tools": OpenAI tool-calling via OpenRouter; structured verdict.
+          INPUT_PER_M_USD = 1.00
-          #   - "neurometric_prose": Neurometric marketplace SLM; prose output + heuristic verdict.
+          OUTPUT_PER_M_USD = 5.00
-          MODELS = [
-              # (slug, display name, input_per_M_USD, output_per_M_USD, is_primary, provider_type)
-              ("anthropic/claude-haiku-4.5",       "Claude Haiku 4.5",                     1.00, 5.00, True,  "openrouter_tools"),
-              ("deepseek/deepseek-chat-v3.1",      "DeepSeek V3.1",                        0.15, 0.75, False, "openrouter_tools"),
-              ("moonshotai/kimi-k2-thinking",      "Kimi K2 Thinking",                     0.60, 2.50, False, "openrouter_tools"),
-              ("neurometric/pr-summarizer",        "Neurometric PR-Summarizer (Qwen3-4B)", 0.00, 0.00, False, "neurometric_prose"),
-          ]
 
           system = """You are the CTO and lead reviewer for the peptiderepo project. You are reviewing a pull request opened by an autonomous agent or human contributor.
 
@@ -229,7 +219,9 @@ jobs:
           user_blocks.append(f"**Changed files:**\n```\n{os.environ['CHANGED_FILES']}\n```\n")
           if os.environ.get("CONVENTIONS", "").strip():
               user_blocks.append(f"# Repo CONVENTIONS.md\n{os.environ['CONVENTIONS']}\n")
-          user_blocks.append(f"# Diff\n```diff\n{os.environ['DIFF']}\n```\n")
+          with open(os.environ["DIFF_PATH"], encoding="utf-8", errors="replace") as _df:
+              _diff_text = _df.read()
+          user_blocks.append(f"# Diff\n```diff\n{_diff_text}\n```\n")
           user_message = "\n\n".join(user_blocks)
 
           tools = [{
@@ -261,218 +253,100 @@ jobs:
               }
           }]
 
-          PER_MODEL_TIMEOUT = 60  # seconds; one hung model should not block siblings
+          body = {
+              "model": MODEL_SLUG,
+              "max_tokens": 2048,
+              "messages": [
+                  {"role": "system", "content": system},
+                  {"role": "user", "content": user_message}
+              ],
+              "tools": tools,
+              "tool_choice": {"type": "function", "function": {"name": "submit_review"}}
+          }
+          req = urllib.request.Request(
+              "https://openrouter.ai/api/v1/chat/completions",
+              data=json.dumps(body).encode(),
+              headers={
+                  "Authorization": f"Bearer {api_key}",
+                  "content-type": "application/json",
+                  "HTTP-Referer": "https://github.com/peptiderepo",
+                  "X-Title": f"peptiderepo CTO reviewer ({MODEL_DISPLAY})"
+              },
+              method="POST"
+          )
 
-          # Heuristic verdict inference for prose-voice models that can't do tool-calling.
+          error = None
-          # Keyword order matters: block markers beat approve markers.
+          review = None
-          PROSE_BLOCK_MARKERS = [
+          cost_cents = 0.0
-              "do not merge", "do not approve", "should not be merged", "reject this",
+          ptok = 0
-              "critical security", "critical issue", "critical vulnerability",
+          ctok = 0
-              "blocker", "blocking issue", "request_changes", "request changes",
-              "**critical**", "sql injection", "must be addressed before",
-          ]
-          PROSE_APPROVE_MARKERS = [
-              "safe to merge", "ready to merge", "no blocking issues", "lgtm",
-              "approve this", "looks good to merge", "no concerns",
-          ]
 
-          def infer_verdict_from_prose(text):
+          try:
-              t = (text or "").lower()
+              with urllib.request.urlopen(req, timeout=60) as resp:
-              if any(m in t for m in PROSE_BLOCK_MARKERS):
+                  data = json.loads(resp.read())
-                  return "REQUEST_CHANGES"
+          except Exception as e:
-              if any(m in t for m in PROSE_APPROVE_MARKERS):
+              error = str(e)[:300]
-                  return "APPROVE"
+              data = {}
-              return "COMMENT"
-
-          def call_openrouter_tools(slug, display, in_rate, out_rate, is_primary):
-              body = {
-                  "model": slug,
-                  "max_tokens": 2048,
-                  "messages": [
-                      {"role": "system", "content": system},
-                      {"role": "user", "content": user_message}
-                  ],
-                  "tools": tools,
-                  "tool_choice": {"type": "function", "function": {"name": "submit_review"}}
-              }
-              req = urllib.request.Request(
-                  "https://openrouter.ai/api/v1/chat/completions",
-                  data=json.dumps(body).encode(),
-                  headers={
-                      "Authorization": f"Bearer {api_key}",
-                      "content-type": "application/json",
-                      "HTTP-Referer": "https://github.com/peptiderepo",
-                      "X-Title": f"peptiderepo CTO reviewer ({display})"
-                  },
-                  method="POST"
-              )
-              try:
-                  with urllib.request.urlopen(req, timeout=PER_MODEL_TIMEOUT) as resp:
-                      data = json.loads(resp.read())
-              except Exception as e:
-                  return {
-                      "slug": slug, "display": display, "is_primary": is_primary,
-                      "provider_type": "openrouter_tools",
-                      "error": str(e)[:300],
-                      "cost_cents": 0,
-                  }
 
+          if not error:
               choice = data.get("choices", [{}])[0].get("message", {})
               tool_calls = choice.get("tool_calls", [])
               if not tool_calls:
-                  return {
+                  error = f"No tool_call in response. Raw content: {str(choice)[:300]}"
-                      "slug": slug, "display": display, "is_primary": is_primary,
+              else:
-                      "provider_type": "openrouter_tools",
+                  try:
-                      "error": f"No tool_call in response. Raw content: {str(choice)[:300]}",
+                      review = json.loads(tool_calls[0]["function"]["arguments"])
-                      "cost_cents": 0,
+                  except Exception as e:
-                  }
+                      error = f"Malformed tool args: {e}"
 
-              try:
+              if not error:
-                  review = json.loads(tool_calls[0]["function"]["arguments"])
+                  usage = data.get("usage", {})
-              except Exception as e:
+                  ptok = usage.get("prompt_tokens", 0)
-                  return {
+                  ctok = usage.get("completion_tokens", 0)
-                      "slug": slug, "display": display, "is_primary": is_primary,
+                  cost_usd = (ptok * INPUT_PER_M_USD / 1_000_000) + (ctok * OUTPUT_PER_M_USD / 1_000_000)
-                      "provider_type": "openrouter_tools",
+                  cost_cents = cost_usd * 100
-                      "error": f"Malformed tool args: {e}",
-                      "cost_cents": 0,
-                  }
 
-              usage = data.get("usage", {})
+          # Build comment
-              ptok = usage.get("prompt_tokens", 0)
+          if error:
-              ctok = usage.get("completion_tokens", 0)
+              heading_verdict = "ERROR"
-              cost_usd = (ptok * in_rate / 1_000_000) + (ctok * out_rate / 1_000_000)
+              lines = [f"## CTO Review — {heading_verdict}", ""]
-              cost_cents = cost_usd * 100
+              lines.append(f"Model failed: `{error}`")
-              return {
-                  "slug": slug, "display": display, "is_primary": is_primary,
-                  "provider_type": "openrouter_tools",
-                  "review": review, "prompt_tokens": ptok, "completion_tokens": ctok,
-                  "cost_cents": cost_cents,
-              }
-
-          def call_neurometric_prose(slug, display, is_primary):
-              nm_key = os.environ.get("NEUROMETRIC_API_KEY", "")
-              if not nm_key:
-                  return {
-                      "slug": slug, "display": display, "is_primary": is_primary,
-                      "provider_type": "neurometric_prose",
-                      "error": "NEUROMETRIC_API_KEY secret not set on this repo",
-                      "cost_cents": 0,
-                  }
-              body = {
-                  "model": slug,
-                  "max_tokens": 2048,
-                  "messages": [
-                      {"role": "system", "content": system},
-                      {"role": "user", "content": user_message},
-                  ],
-              }
-              req = urllib.request.Request(
-                  "https://api.neurometric.ai/v1/chat/completions",
-                  data=json.dumps(body).encode(),
-                  headers={
-                      "Authorization": f"Bearer {nm_key}",
-                      "content-type": "application/json",
-                  },
-                  method="POST",
-              )
-              try:
-                  with urllib.request.urlopen(req, timeout=PER_MODEL_TIMEOUT) as resp:
-                      data = json.loads(resp.read())
-              except Exception as e:
-                  return {
-                      "slug": slug, "display": display, "is_primary": is_primary,
-                      "provider_type": "neurometric_prose",
-                      "error": str(e)[:300],
-                      "cost_cents": 0,
-                  }
-              prose = data.get("choices", [{}])[0].get("message", {}).get("content") or ""
-              verdict = infer_verdict_from_prose(prose)
-              return {
-                  "slug": slug, "display": display, "is_primary": is_primary,
-                  "provider_type": "neurometric_prose",
-                  "review": {"verdict": verdict, "prose": prose},
-                  "prompt_tokens": 0, "completion_tokens": 0,
-                  "cost_cents": 0,
-              }
-
-          def call_model(slug, display, in_rate, out_rate, is_primary, provider_type="openrouter_tools"):
-              if provider_type == "neurometric_prose":
-                  return call_neurometric_prose(slug, display, is_primary)
-              return call_openrouter_tools(slug, display, in_rate, out_rate, is_primary)
-
-          results = []
-          with concurrent.futures.ThreadPoolExecutor(max_workers=len(MODELS)) as pool:
-              futures = [pool.submit(call_model, *m) for m in MODELS]
-              for f in concurrent.futures.as_completed(futures):
-                  results.append(f.result())
-
-          # Order: primary first, then alphabetical for stable comparison
-          results.sort(key=lambda r: (not r.get("is_primary"), r["display"]))
-
-          # Build combined comment
-          primary = next((r for r in results if r.get("is_primary") and "review" in r), None)
-          heading_verdict = primary["review"]["verdict"] if primary else "MIXED"
-
-          lines = [f"## CTO Review — {heading_verdict}", ""]
-          lines.append(f"_A/B harness active: {len(results)} models reviewing in parallel. Primary verdict drives heading; others are advisory._")
-          lines.append("")
-
-          total_cents = 0.0
-          for r in results:
-              lines.append(f"---")
-              primary_tag = " (primary)" if r.get("is_primary") else ""
-              lines.append(f"### {r['display']}{primary_tag}")
-              if "error" in r:
-                  lines.append("")
-                  lines.append(f"⚠️ Model failed: `{r['error']}`")
-                  lines.append("")
-                  continue
-              rev = r["review"]
               lines.append("")
-              if r.get("provider_type") == "neurometric_prose":
+              lines.append(f"_reviewer: {MODEL_DISPLAY}_")
-                  lines.append(f"**Verdict:** {rev['verdict']} _(heuristic, inferred from prose)_")
+          else:
-                  lines.append("")
+              heading_verdict = review.get("verdict", "COMMENT")
-                  # Cap at 6KB to keep PR comments readable; 4B model output is rarely over this
+              lines = [f"## CTO Review — {heading_verdict}", ""]
-                  prose = rev.get("prose", "")
+              lines.append(f"**Verdict:** {heading_verdict}")
-                  if len(prose) > 6000:
-                      prose = prose[:6000] + "\n\n_…output truncated for comment length…_"
-                  lines.append(prose)
-                  lines.append("")
-                  lines.append("_free tier; per-call token usage not tracked_")
-                  lines.append("")
-                  continue
-              lines.append(f"**Verdict:** {rev.get('verdict', 'COMMENT')}")
               lines.append("")
-              lines.append(rev.get("summary") or "_(model returned no summary)_")
+              lines.append(review.get("summary") or "_(model returned no summary)_")
               lines.append("")
-              if rev.get("concerns"):
+              if review.get("concerns"):
                   lines.append("**Concerns:**")
-                  for c in rev["concerns"]:
+                  for c in review["concerns"]:
-                      sev = c["severity"].upper()
+                      sev = c.get("severity", "UNKNOWN").upper()
                       f = f"`{c['file']}`" if c.get("file") else ""
                       lines.append(f"- **{sev}** {f} — {c['issue']}")
                   lines.append("")
-              if rev.get("positives"):
+              if review.get("positives"):
-                  lines.append("**Positives:** " + "; ".join(rev["positives"]))
+                  lines.append("**Positives:** " + "; ".join(review["positives"]))
                   lines.append("")
-              lines.append(f"_tokens in/out: {r['prompt_tokens']}/{r['completion_tokens']} · cost: ${r['cost_cents']/100:.4f}_")
+              lines.append(f"_tokens in/out: {ptok}/{ctok} · cost: ${cost_cents/100:.4f}_")
-              total_cents += r["cost_cents"]
               lines.append("")
 
           lines.append("---")
-          lines.append(f"_Total review cost: **${total_cents/100:.4f}**. A/B roster configured in `.github/workflows/cto-review.yml`._")
+          lines.append(f"_Total review cost: **${cost_cents/100:.4f}**. Reviewer: {MODEL_DISPLAY}. Roster configured in `.github/workflows/cto-review.yml`._")
 
           with open("/tmp/review-body.md", "w") as f:
               f.write("\n".join(lines))
           with open(os.environ["GITHUB_OUTPUT"], "a") as f:
-              f.write(f"added_cents={int(round(total_cents))}\n")
+              f.write(f"added_cents={int(round(cost_cents))}\n")
               f.write(f"skipped=0\n")
               f.write(f"primary_verdict={heading_verdict}\n")
           PY
 
       - name: Post PR review (formal APPROVE / REQUEST_CHANGES / COMMENT)
-        # Uses primary model's verdict as the formal event. Falls back to COMMENT
+        # Uses Haiku's verdict as the formal event. Falls back to COMMENT
-        # if the primary model failed or returned something unexpected.
+        # if the model failed or returned something unexpected.
         if: steps.budget.outputs.skip != 'true' && steps.review.outputs.skipped != '1'
         uses: actions/github-script@v7
         env:

.github/workflows/deploy.yml

@@ -16,88 +16,10 @@ jobs:
     name: Pre-deploy CI
     uses: ./.github/workflows/ci.yml
 
-  deploy-staging:
+  deploy:
-    name: Deploy to Staging
+    name: Deploy (shared pipeline)
     needs: ci
-    runs-on: ubuntu-latest
+    uses: peptiderepo/peptide-e2e/.github/workflows/deploy-app.yml@main
-    environment: staging
+    with:
-    steps:
+      target_path: wp-content/plugins/peptide-repo-core
-      - uses: actions/checkout@v4
+    secrets: inherit
-      - name: Setup SSH key
-        run: |
-          mkdir -p ~/.ssh
-          echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/deploy_key
-          chmod 600 ~/.ssh/deploy_key
-          ssh-keyscan -p ${{ secrets.SSH_PORT }} ${{ secrets.SSH_HOST }} >> ~/.ssh/known_hosts 2>/dev/null
-      - name: Deploy via rsync → staging
-        run: |
-          rsync -avz --delete \
-            --exclude '.git' --exclude '.github' \
-            --exclude 'tests' --exclude 'phpunit.xml.dist' \
-            --exclude 'composer.json' --exclude 'composer.lock' \
-            --exclude 'vendor' --exclude 'phpcs.xml.dist' \
-            --exclude 'ARCHITECTURE.md' --exclude 'CONVENTIONS.md' --exclude 'CHANGELOG.md' \
-            -e "ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }}" \
-            ./ ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }}:~/domains/peptiderepo.com/public_html/staging/wp-content/plugins/peptide-repo-core/
-      - name: Staging health check
-        run: |
-          sleep 5
-          STATUS=$(curl -s -o /dev/null -w "%{http_code}" https://staging.peptiderepo.com/ || echo "000")
-          echo "Staging responded: HTTP $STATUS"
-      - name: Cleanup
-        if: always()
-        run: rm -f ~/.ssh/deploy_key
-
-  smoke:
-    name: Smoke tests (staging)
-    needs: deploy-staging
-    uses: peptiderepo/peptide-e2e/.github/workflows/smoke.yml@main
-    secrets:
-      STAGING_WP_ADMIN_USER: ${{ secrets.STAGING_WP_ADMIN_USER }}
-      STAGING_WP_ADMIN_PASSWORD: ${{ secrets.STAGING_WP_ADMIN_PASSWORD }}
-
-  deploy-production:
-    name: Deploy to Production
-    needs: [ci, deploy-staging, smoke]
-    runs-on: ubuntu-latest
-    environment: production
-    steps:
-      - uses: actions/checkout@v4
-      - name: Setup SSH key
-        run: |
-          mkdir -p ~/.ssh
-          echo "${{ secrets.SSH_PRIVATE_KEY }}" > ~/.ssh/deploy_key
-          chmod 600 ~/.ssh/deploy_key
-          ssh-keyscan -p ${{ secrets.SSH_PORT }} ${{ secrets.SSH_HOST }} >> ~/.ssh/known_hosts 2>/dev/null
-      - name: Deploy via rsync → production
-        run: |
-          rsync -avz --delete \
-            --exclude '.git' --exclude '.github' \
-            --exclude 'tests' --exclude 'phpunit.xml.dist' \
-            --exclude 'composer.json' --exclude 'composer.lock' \
-            --exclude 'vendor' --exclude 'phpcs.xml.dist' \
-            --exclude 'ARCHITECTURE.md' --exclude 'CONVENTIONS.md' --exclude 'CHANGELOG.md' \
-            -e "ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }}" \
-            ./ ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }}:~/domains/peptiderepo.com/public_html/wp-content/plugins/peptide-repo-core/
-      - name: Purge LiteSpeed Cache
-        run: |
-          ssh -i ~/.ssh/deploy_key -p ${{ secrets.SSH_PORT }} \
-            ${{ secrets.SSH_USERNAME }}@${{ secrets.SSH_HOST }} \
-            "cd ~/domains/peptiderepo.com/public_html && find wp-content/litespeed/ -type f -delete 2>/dev/null; touch .lscache_purge 2>/dev/null || true"
-      - name: Production health check
-        run: |
-          sleep 5
-          STATUS=$(curl -s -o /dev/null -w "%{http_code}" https://peptiderepo.com)
-          if [ "$STATUS" != "200" ] && [ "$STATUS" != "403" ]; then
-            echo "ERROR: Site returned HTTP $STATUS"
-            exit 1
-          fi
-          echo "Production healthy (HTTP $STATUS)"
-      - name: Cleanup
-        if: always()
-        run: rm -f ~/.ssh/deploy_key
-      - name: Deploy summary
-        run: |
-          echo "## Deployment Complete" >> $GITHUB_STEP_SUMMARY
-          echo "- **Commit:** \`${GITHUB_SHA::7}\`" >> $GITHUB_STEP_SUMMARY
-          echo "- **Deployed to:** peptiderepo.com" >> $GITHUB_STEP_SUMMARY

.github/workflows/main-push-audit.yml

@@ -29,12 +29,22 @@ jobs:
         with:
           script: |
             const sha = context.sha;
-            const { data: prs } = await github.rest.repos.listPullRequestsAssociatedWithCommit({
+            // Squash-merge -> PR association is eventually-consistent; poll briefly
-              owner: context.repo.owner,
+            // before concluding this was a direct push (avoids false positives on merges).
-              repo: context.repo.repo,
+            async function findMergedPR() {
-              commit_sha: sha,
+              for (let attempt = 1; attempt <= 5; attempt++) {
-            });
+                const { data: prs } = await github.rest.repos.listPullRequestsAssociatedWithCommit({
-            const merged = prs.find(p => p.merged_at);
+                  owner: context.repo.owner,
+                  repo: context.repo.repo,
+                  commit_sha: sha,
+                });
+                const m = prs.find(p => p.merged_at);
+                if (m) return m;
+                if (attempt < 5) await new Promise(r => setTimeout(r, 10000));
+              }
+              return null;
+            }
+            const merged = await findMergedPR();
             if (merged) {
               core.info(`OK: commit ${sha.substring(0,7)} came from PR #${merged.number}`);
               return;

ARCHITECTURE.md

@@ -69,13 +69,20 @@ peptide-repo-core/
 │   ├── class-pr-core-seed-data.php    # Dev fixture: 3 peptides, 10 dosing rows, 5 legal cells
 │   │
 │   ├── cpt/
-│   │   └── class-pr-core-peptide-cpt.php  # CPT + peptide_category registration (guarded), meta fields, sanitizers
+│   │   ├── class-pr-core-peptide-cpt.php       # CPT + peptide_category registration (guarded), meta fields, sanitizers
+│   │   └── class-pr-core-schema-sanitizers.php # Sanitizers for v0.6.0 schema-input meta (formula, weight, aliases, FAQ)
+│   │   └── class-pr-core-repo-daily-cpt.php    # Repo Daily CPT registration for editorial content
+│   │
+│   ├── taxonomies/
+│   │   └── class-pr-core-repo-daily-taxonomy.php  # repo_daily_category taxonomy + term seeding
 │   │
 │   ├── migrations/
 │   │   ├── class-pr-core-migration-runner.php           # Sequential migration engine
 │   │   ├── class-pr-core-migration-0001-dosing-rows.php # pr_dosing_rows table
 │   │   ├── class-pr-core-migration-0002-legal-cells.php # pr_legal_cells table + unique constraint
-│   │   └── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
+│   │   ├── class-pr-core-migration-0003-candidate-queue.php # pr_ai_candidate_queue table
+│   │   ├── class-pr-core-migration-0004-backfill-peptide-meta.php # Backfill _pr_* schema meta from PSA psa_* keys
+│   │   └── class-pr-core-pubchem-client.php              # PubChem REST client (used by migration 0004)
 │   │
 │   ├── dto/
 │   │   ├── class-pr-core-peptide-dto.php     # Typed peptide value object
@@ -90,14 +97,18 @@ peptide-repo-core/
 │   │   └── class-pr-core-candidate-queue-repository.php  # CRUD + approve/reject for queue
 │   │
 │   ├── admin/
-│   │   ├── class-pr-core-admin.php                # Admin initialization, menu, styles
+│   │   ├── class-pr-core-admin.php                    # Admin initialization, menu, styles
-│   │   ├── class-pr-core-peptide-metaboxes.php    # Identifiers, dosing, legal meta boxes
+│   │   ├── class-pr-core-peptide-metaboxes.php        # Identifiers, dosing, legal meta boxes
-│   │   ├── class-pr-core-admin-columns.php        # Evidence, editorial, dosing count columns
+│   │   ├── class-pr-core-repo-daily-metaboxes.php     # Author byline and clinical review flag meta boxes
-│   │   └── class-pr-core-candidate-queue-page.php # AI candidate review admin screen
+│   │   ├── class-pr-core-admin-columns.php            # Evidence, editorial, dosing count columns
+│   │   └── class-pr-core-candidate-queue-page.php     # AI candidate review admin screen
 │   │
 │   ├── frontend/
-│   │   ├── class-pr-core-disclaimer.php   # Shortcode + static API for surface disclaimers
+│   │   ├── class-pr-core-disclaimer.php       # Shortcode + static API for surface disclaimers
-│   │   └── class-pr-core-jsonld.php       # schema.org Drug JSON-LD on single peptide pages
+│   │   ├── class-pr-core-jsonld.php           # Orchestrator: Yoast-integrated Drug/FAQ/MedicalWebPage emission
+│   │   ├── class-pr-core-jsonld-drug.php      # Drug (+ MolecularEntity) schema piece builder
+│   │   ├── class-pr-core-jsonld-webpage.php   # MedicalWebPage retype + lastReviewed/reviewedBy enrichment
+│   │   └── class-pr-core-jsonld-faq.php       # FAQPage schema piece (emits only when _pr_faq_items populated)
 │   │
 │   └── api/
 │       └── class-pr-core-rest-controller.php  # REST endpoints for peptides, dosing, legal
@@ -110,6 +121,17 @@ peptide-repo-core/
 
 ---
 
+## Content Types
+
+| CPT | Slug | Taxonomy | Purpose | Registrant |
+|-----|------|----------|---------|-----------|
+| `peptide` | `/peptides/[slug]/` | `peptide_category` | Canonical peptide monographs with dosing, legal, evidence metadata | PR Core v0.2.0 (consolidated from PSA) |
+| `repo_daily` | `/daily/[slug]/` | `repo_daily_category` | Editorial publications (articles, guides, comparisons, news) generated by PRAutoBlogger, published under Boo Sheeran byline | PR Core v0.5.0 |
+
+**Verification scanner scope:** The verification scanner (class-pr-core-verification-scanner.php) queries `post_type=peptide` only. `repo_daily` posts are excluded automatically by CPT separation and do not appear in the overdue queue.
+
+---
+
 ## Custom Tables
 
 ### `{prefix}pr_dosing_rows`
@@ -181,9 +203,27 @@ Automated extraction populates the queue; humans approve/reject. Approved rows c
 ### #5: Disclaimer component owned by core
 Single editorial review point. All consumer plugins render the same versioned disclaimer text. Surface-specific copy (dosing, legal, reconstitution, AI answer) stored in one wp_option.
 
-### #6: JSON-LD from day one
+### #6: JSON-LD from day one (v0.6.0: Yoast-integrated)
 Drug schema on single pages increases LLM citation rate. Filter hook allows consumer plugins to extend the schema object.
 
+**v0.6.0 Yoast integration (ratified jsonld-contract-v1 2026-06-11):**
+
+- **Integrated path (Yoast active):** PR Core hooks into `wpseo_schema_graph_pieces` (priority 11) to inject Drug and FAQPage pieces. Yoast owns `WebPage`/`BreadcrumbList` — we never emit those. `wpseo_schema_webpage_type` filter retypes the page node to `MedicalWebPage`. `wpseo_schema_graph` (priority 11) enriches the existing WebPage piece with `lastReviewed`, `reviewedBy`, and `audience`.
+- **Standalone fallback (no Yoast):** `wp_head` action (priority 99) emits a complete `@graph` (Drug + FAQPage) only. Suppressed automatically when `function_exists('YoastSEO')` is true.
+- **Drug `@id`:** `{permalink}#drug` — stable for cross-plugin `about` linkage from PRAutoBlogger articles.
+- **Molecular data source:** `_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases` (written by migration 0004, sourced from PSA `psa_*` keys or PubChem REST API).
+- **FAQ emission:** `_pr_faq_items` post-meta (JSON array of `{question, answer}` objects). Node emitted only when items exist.
+- **Dosing omitted from schema:** YMYL constraint — no dosing data in JSON-LD.
+
+JSON-LD class tree (v0.6.0):
+
+| Class | File | Responsibility |
+|---|---|---|
+| `PR_Core_Jsonld` | `frontend/class-pr-core-jsonld.php` | Orchestrator: registers hooks, Yoast vs. standalone routing |
+| `PR_Core_Jsonld_Drug` | `frontend/class-pr-core-jsonld-drug.php` | Builds Drug (+ MolecularEntity) schema node |
+| `PR_Core_Jsonld_Webpage` | `frontend/class-pr-core-jsonld-webpage.php` | MedicalWebPage retype + lastReviewed/reviewedBy enrichment |
+| `PR_Core_Jsonld_Faq` | `frontend/class-pr-core-jsonld-faq.php` | FAQPage node (emit-only-when-populated) |
+
 ### #7: PR Core owns the `peptide` CPT and `peptide_category` taxonomy (v0.2.0)
 Prior to v0.2.0, PR Core registered `pr_peptide` while Peptide Search AI registered `peptide` — both claimed the public rewrite slug `peptides`, and WP's rewrite resolver picked PR Core's empty CPT, 404'ing all 89 production peptide detail pages. v0.2.0 consolidates both registrations onto a single `peptide` CPT, owned by PR Core. PSA v4.5.0 drops its CPT/taxonomy registration; its meta boxes (`psa_peptide_data`, `psa_extended_data`), directory shortcode, KB article renderer, and search widget continue operating on the shared `peptide` CPT regardless of who registers it. Registration on both sides is guarded with `post_type_exists()` / `taxonomy_exists()` so deploy order is forgiving.
 
@@ -196,3 +236,4 @@ PR Core `uninstall.php` removes plugin-owned data only:
 3. **Does not delete `peptide_category` terms.** Shared-ownership taxonomy; term metadata the site relies on outlasts this plugin.
 4. **Deletes `pr_core_*` options.**
 5. **Removes `manage_peptide_content` capability from all roles.**
+6. **Deletes v0.6.0 schema-input meta keys** (`_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items`) from all peptide posts. These are PR Core-authored values (sourced from PubChem / PSA) and are safe to remove on uninstall. They do not overlap with PSA's `psa_*` namespace — PSA's own meta is unaffected.

CHANGELOG.md

@@ -3,6 +3,87 @@
 All notable changes to Peptide Repo Core are documented here.
 Format: [Semantic Versioning](https://semver.org/).
 
+## [0.6.2] — 2026-06-13
+
+### Fixed
+- **Critical**: Peptide monograph pages (e.g. `/peptides/bpc-157/`) returned HTTP 500 after v0.6.0 launch. Root cause: `PR_Core_Jsonld::inject_graph_pieces()` appended plain PHP arrays (Drug, FAQ) to Yoast's `wpseo_schema_graph_pieces` filter. Yoast's `Schema_Generator::filter_graph_pieces_to_generate()` then called `get_class()` and `is_needed()` on every piece, expecting `Abstract_Schema_Piece` objects — a plain array causes `PHP Fatal: get_class(): Argument #1 ($object) must be of type object, array given`. Non-peptide pages (/, /about/, /peptides/ archive) were unaffected because the `is_singular('peptide')` guard prevented entry.
+- Fix: removed `wpseo_schema_graph_pieces` hook entirely. Drug and FAQPage nodes are now injected via a new `inject_graph_nodes()` method hooked on `wpseo_schema_graph` at priority 12, which receives Yoast's fully-assembled graph as an array of plain arrays — safe for plain array appends.
+- Added regression test `tests/unit/test-jsonld-peptide-piece.php` that reproduces the v0.6.1 `get_class(array)` fatal and verifies the v0.6.2 `inject_graph_nodes` path emits Drug + FAQ correctly across peptide, non-peptide, and empty-FAQ scenarios.
+
+### Changed
+- `PR_Core_Jsonld::register_hooks()`: no longer registers `wpseo_schema_graph_pieces`; registers `wpseo_schema_graph` at priority 12 for Drug/FAQ injection (in addition to priority 11 for `enrich_webpage_piece`, unchanged).
+- `PR_Core_Jsonld::inject_graph_pieces()` renamed to `inject_graph_nodes()`; signature updated from `(array $pieces, $context)` to `(array $graph, $context)` to reflect that it now receives the assembled graph, not the pieces array.
+
+
+
+## [0.6.1] — 2026-06-13
+
+### Fixed
+- Fix: Yoast `wpseo_schema_webpage_type` passes `string|array` on singulars — accept `string|array` in `retype_to_medical_webpage()` signature; return type updated to match (PHP 8.1+ union). Eliminates `TypeError` → HTTP 500 on all singular pages (monographs + plain Pages) under `strict_types=1`.
+- Fix: `enrich_webpage_piece` compared `'WebPage' === $piece['@type']` but Yoast sets `@type` as an array on singular pages. Normalise `@type` to array before `in_array()` check; `lastReviewed`, `reviewedBy`, and `audience` now inject correctly.
+- Add regression test `tests/unit/test-jsonld-webpage.php`: exercises `retype_to_medical_webpage()` with array input for peptide and non-peptide contexts (no TypeError), and `enrich_webpage_piece` with `@type` as array (enrichment injects). Tests fail against v0.6.0, pass after fix.
+
+## [0.6.0] — 2026-06-13
+
+### Added
+- **Backfill migration 0004** (`class-pr-core-migration-0004-backfill-peptide-meta.php`): Copies PSA-stored PubChem data into new `_pr_*` schema-input meta keys across all published peptide posts. Source: `psa_molecular_formula` → `_pr_molecular_formula`, `psa_molecular_weight` → `_pr_molecular_weight` (strip "Da", floatval), `psa_aliases` → `_pr_aliases` (comma-split, sanitize, JSON array). For 4 posts without PSA data (igf-1-lr3, cagrilintide, ghk-cu, epitalon), falls back to PubChem REST API via new `PR_Core_Pubchem_Client`. Migration is idempotent + re-runnable; skips posts where all three keys are already populated.
+- **Schema-input meta keys** (registered in CPT, v0.6.0):
+  - `_pr_molecular_formula` — sanitized molecular formula string.
+  - `_pr_molecular_weight` — float as string (g/mol); "Da" suffix normalized out.
+  - `_pr_aliases` — JSON array of sanitized alternate names.
+  - `_pr_faq_items` — JSON array of `{question, answer}` objects for FAQPage emission.
+- **`PR_Core_Schema_Sanitizers`** (`cpt/class-pr-core-schema-sanitizers.php`): Static sanitizers for the four schema-input meta keys, split from `PR_Core_Peptide_CPT` to keep the CPT file under 300 lines.
+- **`PR_Core_Pubchem_Client`** (`migrations/class-pr-core-pubchem-client.php`): Lightweight PubChem REST client with CID/name lookup, synonym fetch, and MAX_RETRIES=3 exponential backoff. Used exclusively by migration 0004.
+- **Yoast-integrated JSON-LD emission** (replaces standalone `wp_head` script):
+  - `PR_Core_Jsonld_Drug` — builds Drug (+ MolecularEntity) schema node with stable `@id = {permalink}#drug`, reads `_pr_*` schema-input meta, `alternateName`/`molecularFormula`/`molecularWeight` (g/mol) emitted only when non-empty.
+  - `PR_Core_Jsonld_Webpage` — retypes Yoast's WebPage to `MedicalWebPage` via `wpseo_schema_webpage_type`; enriches it with `lastReviewed`, `reviewedBy` (Person or Organization), and `audience` via `wpseo_schema_graph`.
+  - `PR_Core_Jsonld_Faq` — builds FAQPage node from `_pr_faq_items`; emitted only when items exist.
+  - `PR_Core_Jsonld` — orchestrator hooking all three builders into Yoast's graph; maintains standalone `@graph` fallback when Yoast is inactive.
+- **`CONTEXT.md`** — new domain glossary covering all new terms (`_pr_*` keys, Drug node, MedicalWebPage, FAQPage, Yoast integration contract, PubChem CID).
+
+### Changed
+- `PR_Core_Jsonld` rewritten: replaces standalone `wp_head` script-tag emission with Yoast graph-filter integration. Standalone `@graph` retained as fallback only. **No duplicate WebPage/BreadcrumbList** — Yoast owns those.
+- `PR_Core_Peptide_CPT::get_meta_fields()` — adds 4 new `_pr_*` fields; existing `aliases`/`molecular_formula`/`molecular_weight` fields unchanged.
+- `PR_Core_Migration_Runner::MIGRATIONS` — adds `PR_Core_Migration_0004_Backfill_Peptide_Meta` at index 3.
+- `PR_CORE_TARGET_SCHEMA_VERSION` bumped from 3 to 4.
+- `uninstall.php` — purges `_pr_molecular_formula`, `_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items` from all peptide posts on uninstall.
+- `ARCHITECTURE.md` — §#6 JSON-LD rewritten; §2.9 uninstall spec updated; file tree updated for new classes.
+- `CONVENTIONS.md` — schema-input meta convention added; Yoast JSON-LD extension pattern added.
+
+### Fixed
+- `tests/unit/test-migration-0004.php`: `error_log()` stub now guarded with `function_exists()` to prevent PHP fatal redeclaration error in CI PHP Lint (8.1/8.2/8.3).
+- `tests/bootstrap.php`: `wp_json_encode` stub updated to accept `int $flags = 0` second argument, matching production call signature; guarded with `function_exists()`.
+- `cpt/class-pr-core-schema-sanitizers.php`: `sanitize_molecular_formula()` rewritten from character-allowlist to element-formula grammar validation (Option B). Now strips control characters first, then extracts the maximal leading run of valid `[A-Z][a-z]?\d*` element tokens and group separators. Inputs containing trailing English words (e.g., `"C10H12\ninjection"`) correctly return the formula prefix only (`"C10H12"`); fully invalid inputs (e.g., `"<script>alert(1)</script>"`) return `""`. Parenthesised formulas (e.g., `"C2H5(OH)"`) preserved unchanged. Seven-case unit test coverage added.
+
+### Technical
+- Schema version: `PR_CORE_TARGET_SCHEMA_VERSION` = 4.
+- New test files: `tests/unit/test-migration-0004.php`, `tests/unit/test-jsonld.php`.
+- Yoast filter names verified against Yoast 27.6: `wpseo_schema_graph_pieces`, `wpseo_schema_webpage_type`, `wpseo_schema_graph`.
+- No CAS/DrugBank emission in v0.6.0 (no reliable source — documented in ARCHITECTURE.md for future enrichment sprint).
+
+## [0.5.0] — 2026-04-27
+
+### Added
+- **Repo Daily CPT**: New `repo_daily` custom post type at `/daily/[slug]/` for editorial publications (articles, guides, comparisons, news) generated by PRAutoBlogger and published under the Boo Sheeran byline.
+- **Repo Daily Category Taxonomy**: Non-hierarchical `repo_daily_category` taxonomy with four seeded terms (article, guide, comparison, news) for editorial classification.
+- **Repo Daily Meta Fields**:
+  - `_repo_daily_author` (string, default "Boo Sheeran") — byline displayed in theme templates. Never hardcoded; always read from meta.
+  - `_repo_daily_clinical_review_required` (bool, stored as '1'/'') — editorial flag marking posts that require PR Clinical Review before publication.
+- **Repo Daily Admin Meta Box**: "Article Settings" meta box on repo_daily edit screen with author byline field and clinical review flag checkbox.
+- **Bulk Author Migration**: On activation, sets `_repo_daily_author = 'Boo Sheeran'` on all post_type=post posts bearing the psa_source meta key (autoblogged articles). Idempotent; existing meta values preserved. Posts remain post_type=post; forward-only migration for byline retroactivity.
+
+### Changed
+- `PR_Core_Admin::register_hooks()` now registers repo_daily metaboxes alongside peptide metaboxes.
+
+### Technical
+- New classes: `PR_Core_Repo_Daily_CPT`, `PR_Core_Repo_Daily_Taxonomy`, `PR_Core_Repo_Daily_Metaboxes`.
+- New method: `PR_Core_Activator::migrate_autoblogged_author_meta()` — idempotent bulk meta setter.
+- Taxonomy seeding: `PR_Core_Repo_Daily_Taxonomy::seed_terms()` called on activation.
+
+### Documentation
+- ARCHITECTURE.md: Added repo_daily CPT to content-type table; documented scanner exclusion by CPT separation.
+- CONVENTIONS.md: Added "How to add a new post meta field to repo_daily posts" extension pattern.
+
 ## [0.4.0] — 2026-04-27
 
 ### Added

CONTEXT.md

@@ -0,0 +1,115 @@
+# Peptide Repo Core — Domain Glossary (CONTEXT.md)
+
+This file defines domain terms introduced or used in the peptide-repo-core codebase.
+Per AGENT-OPERATING-STANDARD v1.2.0, update this file in the same PR as any change
+that introduces, renames, or redefines a domain term.
+
+---
+
+## Peptide
+
+A short chain of amino acids studied for biological activity. In this codebase, a
+"peptide" refers to one of the 93 canonical monograph posts (`post_type = 'peptide'`)
+on peptiderepo.com. Each monograph covers identity, mechanism, evidence, and regulatory
+status. **No dosing data appears in schema output** (YMYL constraint).
+
+## Monograph
+
+A single-peptide page (`/peptides/{slug}/`) containing the canonical research profile
+for that compound. Populated from the `peptide` CPT plus its associated meta fields,
+dosing rows (`pr_dosing_rows` table), and legal cells (`pr_legal_cells` table).
+
+## Drug node
+
+The `schema.org/Drug` structured-data entity emitted on each monograph page. Stable
+`@id` is `{permalink}#drug` — this URI is the cross-plugin linking target used by
+PRAutoBlogger article `about` references (per `jsonld-contract-v1`, ratified 2026-06-11).
+
+## MedicalWebPage
+
+A `schema.org/MedicalWebPage` subtype of `WebPage`. Applied to peptide monograph pages
+via the `wpseo_schema_webpage_type` Yoast filter. Signals to search engines and LLMs
+that the page carries medical/scientific content reviewed by an organization.
+
+## FAQPage
+
+A `schema.org/FAQPage` node emitted when `_pr_faq_items` post-meta is populated.
+Contains `Question`/`Answer` pairs curated by the CMO content sprint (v0.6.0 ships
+the meta key and emitter; population is a separate sprint). Emitted only when items
+exist — never an empty node.
+
+## _pr_molecular_formula
+
+Post-meta key (string). Stores the molecular formula of a peptide compound
+(e.g., `C62H98N16O22`). Written by migration 0004 from PSA's `psa_molecular_formula`
+key. Sanitized: only `[A-Za-z0-9().\[\]{}]` characters allowed.
+
+## _pr_molecular_weight
+
+Post-meta key (string). Stores the molecular weight of a peptide compound as a
+float string (e.g., `"1419.5"`). Unit: g/mol (equivalent to Da, but g/mol is the
+standard SI label used in schema.org `QuantitativeValue`). Written by migration 0004
+from PSA's `psa_molecular_weight` — "Da" suffix stripped, `floatval()` applied.
+
+## _pr_aliases
+
+Post-meta key (string, JSON array). Stores alternate names / synonyms for a peptide
+(e.g., `'["Body Protection Compound-157","PL 14736","Bepecin"]'`). Written by
+migration 0004 from PSA's comma-separated `psa_aliases`. Each alias sanitized via
+`sanitize_text_field`. Maps to `schema.org/alternateName` array on the Drug node.
+
+## _pr_faq_items
+
+Post-meta key (string, JSON array of objects). Stores curated FAQ entries for a
+peptide monograph, each as `{question: string, answer: string}`. Registered in v0.6.0;
+population is a CMO content sprint. Maps to `schema.org/FAQPage` when non-empty.
+Sanitized by `PR_Core_Schema_Sanitizers::sanitize_faq_items()` on save.
+Purged on uninstall.
+
+## Schema-input meta
+
+The collective term for the four `_pr_*` meta keys (`_pr_molecular_formula`,
+`_pr_molecular_weight`, `_pr_aliases`, `_pr_faq_items`) introduced in v0.6.0. These
+are the data-layer inputs to the JSON-LD emitter. The emitter reads only these keys
+at render time — it never reads PSA's `psa_*` keys directly (no cross-plugin read
+coupling). Sourced from PSA via migration 0004 (one-time backfill).
+
+## psa_* meta
+
+Post-meta keys written by Peptide Search AI (PSA) plugin using its PubChem integration.
+Includes `psa_molecular_formula`, `psa_molecular_weight`, `psa_aliases`,
+`psa_pubchem_cid`, `psa_cas_number`, `psa_drugbank_id`. Migration 0004 treats all
+`psa_*` values as UNTRUSTED and sanitizes them before writing to PR Core's `_pr_*` keys.
+PR Core never reads `psa_*` keys at render time.
+
+## PubChem CID
+
+A numeric compound identifier in the NCBI PubChem database (e.g., `9941957` for
+BPC-157). Used by migration 0004 as a fallback lookup for the 4 peptide posts that
+lack `psa_molecular_formula`. Fetched via `PR_Core_Pubchem_Client`.
+
+## Yoast integration contract
+
+The agreed schema architecture ratified 2026-06-11 (`convo/prcore/decisions/2026-06-11-jsonld-contract-v1.md`):
+PR Core integrates into Yoast's schema graph via `wpseo_schema_*` filters; never
+emits duplicate `WebPage` or `BreadcrumbList` nodes; maintains a standalone `@graph`
+fallback for when Yoast is inactive. The Drug `@id` convention (`{permalink}#drug`)
+is part of this contract.
+
+## Evidence strength
+
+Ordered enum: `preclinical`, `case-series`, `observational`, `rct-small`, `rct-large`,
+`meta-analysis`. Stored in the `evidence_strength` post-meta key. Does **not** appear
+in schema.org output (dosing/evidence YMYL constraint).
+
+## Verdict
+
+One of five editorial states assigned to a monograph: `effective`, `promising`,
+`mixed`, `insufficient_evidence`, `avoid`. Stored in post content via a verdict card
+Gutenberg block. Not surfaced in JSON-LD (dosing YMYL constraint).
+
+## Migration runner
+
+`PR_Core_Migration_Runner` — runs numbered migrations (0001–N) sequentially on every
+`plugins_loaded`. Compares `pr_core_schema_version` wp_option against
+`PR_CORE_TARGET_SCHEMA_VERSION` constant. All migrations are idempotent and re-runnable.

CONVENTIONS.md

@@ -14,13 +14,22 @@
 Autoloader convention: `PR_Core_Foo_Bar` maps to `class-pr-core-foo-bar.php`.
 Files live in `includes/` or one level of subdirectory under `includes/`.
 
-## How To: Add a New Post-Meta Field
+## How To: Add a New Post-Meta Field to Peptide Posts
 
 1. Add the field to `PR_Core_Peptide_CPT::get_meta_fields()` in `cpt/class-pr-core-peptide-cpt.php`.
 2. Add the field to `PR_Core_Peptide_DTO` constructor and `to_array()` in `dto/class-pr-core-peptide-dto.php`.
 3. Add the field to `PR_Core_Peptide_Repository::post_to_dto()` in `repositories/class-pr-core-peptide-repository.php`.
 4. Add a form input in `PR_Core_Peptide_Metaboxes::render_identifiers_box()` in `admin/class-pr-core-peptide-metaboxes.php`.
 5. The `save_meta()` method reads from the same field list — no changes needed unless custom save logic applies.
+6. **Schema-input meta fields** (`_pr_*` keys introduced in v0.6.0) use `PR_Core_Schema_Sanitizers` as the sanitize_callback. Add new sanitizers to `cpt/class-pr-core-schema-sanitizers.php`, not to `PR_Core_Peptide_CPT` (keeps CPT under 300 lines).
+7. If the field is purged on uninstall, add it to the `$schema_meta_keys` array in `uninstall.php`.
+
+## How To: Add a New Post-Meta Field to Repo Daily Posts
+
+1. Define the meta key (start with `_repo_daily_`) and sanitization logic (use `sanitize_text_field()` for strings, cast to bool for checkboxes).
+2. Create a new metabox or extend `PR_Core_Repo_Daily_Metaboxes::render_meta_box()` in `admin/class-pr-core-repo-daily-metaboxes.php`.
+3. In `PR_Core_Repo_Daily_Metaboxes::save_meta()`, handle the field: read from `$_POST`, sanitize, and call `update_post_meta()`.
+4. Example: The `_repo_daily_clinical_review_required` checkbox checks for `isset( $_POST['key'] )` and stores `'1'` or `''`; `get_post_meta()` is type-safe because the value is always one of two strings, never a bool.
 
 ## How To: Add a New Migration
 
@@ -29,6 +38,7 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 3. Add the class name to `PR_Core_Migration_Runner::MIGRATIONS` array (index = version - 1).
 4. Bump `PR_CORE_TARGET_SCHEMA_VERSION` in `peptide-repo-core.php`.
 5. All migrations must be idempotent (safe to run twice).
+6. **Idempotency caveat (all-or-nothing skip):** migration 0004's skip guard requires *all* populated keys; a post with legitimately empty aliases will re-run on manual re-invoke — this is safe (write_meta only overwrites with non-empty values) but expected.
 
 ## How To: Add a New REST Endpoint
 
@@ -43,6 +53,16 @@ Files live in `includes/` or one level of subdirectory under `includes/`.
 2. Use `[pr_disclaimer surface="new-surface"]` in templates.
 3. Custom copy can be set via `PR_Core_Disclaimer::update_disclaimer()`.
 
+## How To: Extend the JSON-LD Drug Schema
+
+v0.6.0 uses four focused classes (see ARCHITECTURE.md §#6). To add a new field to the Drug node:
+
+1. Add the logic to `PR_Core_Jsonld_Drug::build()` in `includes/frontend/class-pr-core-jsonld-drug.php`.
+2. Read data from the appropriate `_pr_*` post-meta key (not from PSA `psa_*` keys directly).
+3. **Always omit the field when the meta is empty** — never emit blank/null/zero values.
+4. To add a new schema piece (not Drug), create a new `PR_Core_Jsonld_<Piece>` class in `frontend/` and inject it from `PR_Core_Jsonld::inject_graph_pieces()`.
+5. The `pr_core_jsonld_peptide` filter on the Drug node array is preserved for consumer plugins.
+
 ## Error Handling
 
 - Repository methods return `null` or `0` on failure, never throw.

includes/admin/class-pr-core-admin.php

@@ -34,6 +34,11 @@ class PR_Core_Admin {
 		add_filter( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_columns', [ $columns, 'add_columns' ] );
 		add_action( 'manage_' . PR_Core_Peptide_CPT::POST_TYPE . '_posts_custom_column', [ $columns, 'render_column' ], 10, 2 );
 
+		// Repo Daily meta boxes.
+		$repo_daily_metaboxes = new PR_Core_Repo_Daily_Metaboxes();
+		add_action( 'add_meta_boxes', [ $repo_daily_metaboxes, 'add_meta_boxes' ] );
+		add_action( 'save_post_' . PR_Core_Repo_Daily_CPT::POST_TYPE, [ $repo_daily_metaboxes, 'save_meta' ], 10, 2 );
+
 		add_action( 'admin_menu', [ $this, 'add_admin_pages' ] );
 		add_action( 'admin_enqueue_scripts', [ $this, 'enqueue_admin_styles' ] );
 	}

includes/admin/class-pr-core-repo-daily-metaboxes.php

@@ -0,0 +1,113 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Meta boxes for Repo Daily edit screen: author and clinical review flag.
+ *
+ * What: Renders and saves two meta fields on the repo_daily edit screen.
+ * Who calls it: PR_Core_Admin via add_meta_boxes and save_post hooks.
+ * Dependencies: None.
+ *
+ * Meta fields:
+ * - `_repo_daily_author` (string, default "Boo Sheeran") — byline displayed in templates.
+ * - `_repo_daily_clinical_review_required` (bool, stored as '1'/'') — editorial flag.
+ *
+ * @see admin/class-pr-core-admin.php — Registers these hooks.
+ * @see cpt/class-pr-core-repo-daily-cpt.php — CPT definition.
+ */
+class PR_Core_Repo_Daily_Metaboxes {
+
+	/** @var string Default author byline for Repo Daily articles. */
+	private const DEFAULT_AUTHOR = 'Boo Sheeran';
+
+	/**
+	 * Register meta box on the repo_daily edit screen.
+	 *
+	 * @return void
+	 */
+	public function add_meta_boxes(): void {
+		add_meta_box(
+			'pr-core-repo-daily-meta',
+			__( 'Article Settings', 'peptide-repo-core' ),
+			[ $this, 'render_meta_box' ],
+			PR_Core_Repo_Daily_CPT::POST_TYPE,
+			'normal',
+			'default'
+		);
+	}
+
+	/**
+	 * Render the Article Settings meta box.
+	 *
+	 * @param \WP_Post $post Current post.
+	 * @return void
+	 */
+	public function render_meta_box( \WP_Post $post ): void {
+		wp_nonce_field( 'pr_core_repo_daily_meta', 'pr_core_repo_daily_nonce' );
+
+		$author = sanitize_text_field(
+			get_post_meta( $post->ID, '_repo_daily_author', true ) ?: self::DEFAULT_AUTHOR
+		);
+		$requires_review = get_post_meta( $post->ID, '_repo_daily_clinical_review_required', true );
+
+		echo '<table class="form-table pr-core-meta-table">';
+
+		// Author field.
+		printf(
+			'<tr><th><label for="pr_core_repo_daily_author">%s</label></th><td><input type="text" id="pr_core_repo_daily_author" name="pr_core_repo_daily_author" value="%s" class="regular-text" /></td></tr>',
+			esc_html__( 'Author / Byline', 'peptide-repo-core' ),
+			esc_attr( $author )
+		);
+
+		// Clinical review flag.
+		printf(
+			'<tr><th><label for="pr_core_repo_daily_clinical_review_required">%s</label></th><td><input type="checkbox" id="pr_core_repo_daily_clinical_review_required" name="pr_core_repo_daily_clinical_review_required" value="1" %s /> <span class="description">%s</span></td></tr>',
+			esc_html__( 'Clinical Review Required', 'peptide-repo-core' ),
+			checked( $requires_review, '1', false ),
+			esc_html__( 'Flag for PR Clinical Review before publish', 'peptide-repo-core' )
+		);
+
+		echo '</table>';
+	}
+
+	/**
+	 * Save repo_daily meta fields on post save.
+	 *
+	 * Side effects: updates post meta.
+	 *
+	 * @param int      $post_id Post ID.
+	 * @param \WP_Post $post    Post object.
+	 * @return void
+	 */
+	public function save_meta( int $post_id, \WP_Post $post ): void {
+		if ( ! isset( $_POST['pr_core_repo_daily_nonce'] ) ) {
+			return;
+		}
+
+		if ( ! wp_verify_nonce( sanitize_text_field( wp_unslash( $_POST['pr_core_repo_daily_nonce'] ) ), 'pr_core_repo_daily_meta' ) ) {
+			return;
+		}
+
+		if ( ! current_user_can( 'edit_posts' ) ) {
+			return;
+		}
+
+		if ( defined( 'DOING_AUTOSAVE' ) && DOING_AUTOSAVE ) {
+			return;
+		}
+
+		// Save author field.
+		if ( isset( $_POST['pr_core_repo_daily_author'] ) ) {
+			$author = sanitize_text_field( wp_unslash( $_POST['pr_core_repo_daily_author'] ) );
+			// Use default if empty.
+			if ( empty( $author ) ) {
+				$author = self::DEFAULT_AUTHOR;
+			}
+			update_post_meta( $post_id, '_repo_daily_author', $author );
+		}
+
+		// Save clinical review flag.
+		$requires_review = isset( $_POST['pr_core_repo_daily_clinical_review_required'] ) ? '1' : '';
+		update_post_meta( $post_id, '_repo_daily_clinical_review_required', $requires_review );
+	}
+}

includes/class-pr-core-activator.php

@@ -37,9 +37,17 @@ class PR_Core_Activator {
 		PR_Core_Peptide_CPT::register_peptide_post_type();
 		PR_Core_Peptide_CPT::register_taxonomies();
 
+		// Register repo_daily CPT and taxonomy + seed terms.
+		PR_Core_Repo_Daily_CPT::register_post_type();
+		PR_Core_Repo_Daily_Taxonomy::register_taxonomy();
+		PR_Core_Repo_Daily_Taxonomy::seed_terms();
+
 		// Grant manage_peptide_content to administrators and editors.
 		self::add_capabilities();
 
+		// Bulk-set _repo_daily_author on existing posts with psa_source meta.
+		self::migrate_autoblogged_author_meta();
+
 		// Flush rewrite rules for the new CPT.
 		flush_rewrite_rules( false );
 
@@ -94,4 +102,58 @@ class PR_Core_Activator {
 			}
 		}
 	}
+
+	/**
+	 * Bulk-set _repo_daily_author on autoblogged posts.
+	 *
+	 * Sets `_repo_daily_author = 'Boo Sheeran'` on all post_type=post posts
+	 * that have the psa_source meta key present (identifying them as autoblogged).
+	 * Idempotent: skips posts that already have the meta set.
+	 *
+	 * Side effects: updates post meta in database.
+	 *
+	 * @return void
+	 */
+	private static function migrate_autoblogged_author_meta(): void {
+		global $wpdb;
+
+		// Query all posts of type 'post' that have the psa_source meta key.
+		// phpcs:disable WordPress.DB.DirectDatabaseQuery.DirectQuery
+		// phpcs:disable WordPress.DB.DirectDatabaseQuery.NoCaching
+		$post_ids = $wpdb->get_col(
+			$wpdb->prepare(
+				"SELECT DISTINCT pm.post_id
+				 FROM {$wpdb->postmeta} pm
+				 WHERE pm.meta_key = %s
+				 AND pm.post_id IN (
+					SELECT ID FROM {$wpdb->posts}
+					WHERE post_type = %s
+				 )",
+				'psa_source',
+				'post'
+			)
+		);
+		// phpcs:enable WordPress.DB.DirectDatabaseQuery.DirectQuery
+		// phpcs:enable WordPress.DB.DirectDatabaseQuery.NoCaching
+
+		if ( empty( $post_ids ) ) {
+			return;
+		}
+
+		$author_value = 'Boo Sheeran';
+
+		foreach ( $post_ids as $post_id ) {
+			$post_id = (int) $post_id;
+
+			// Skip if already set (idempotent).
+			$existing = get_post_meta( $post_id, '_repo_daily_author', true );
+			if ( ! empty( $existing ) ) {
+				continue;
+			}
+
+			// Set the author meta.
+			update_post_meta( $post_id, '_repo_daily_author', $author_value );
+		}
+	}
 }
+

includes/class-pr-core.php

@@ -35,6 +35,14 @@ class PR_Core {
 		$topic_tax = new PR_Core_Topic_Taxonomy();
 		$topic_tax->register_hooks();
 
+		// Register repo_daily CPT (fires on init).
+		$repo_daily_cpt = new PR_Core_Repo_Daily_CPT();
+		$repo_daily_cpt->register_hooks();
+
+		// Register repo_daily_category taxonomy (fires on init).
+		$repo_daily_tax = new PR_Core_Repo_Daily_Taxonomy();
+		$repo_daily_tax->register_hooks();
+
 		// One-shot rewrite flush on in-place version bumps. Runs at the very
 		// end of init (priority 999) so all CPTs/taxonomies — ours and
 		// anyone else's — are registered first. Handles updates deployed

includes/cpt/class-pr-core-peptide-cpt.php

@@ -68,7 +68,7 @@ class PR_Core_Peptide_CPT {
 			'aliases'                 => [
 				'type'     => 'string',
 				'default'  => '[]',
-				'sanitize' => [ __CLASS__, 'sanitize_json_array' ],
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
 			],
 			'molecular_formula'       => [
 				'type'     => 'string',
@@ -145,6 +145,28 @@ class PR_Core_Peptide_CPT {
 				'default'  => 'current',
 				'sanitize' => [ PR_Core_Verification_Sanitizers::class, 'sanitize_status' ],
 			],
+			// Schema-input meta (v0.6.0): molecular data sourced from PSA psa_* keys via migration 0004.
+			'_pr_molecular_formula'     => [
+				'type'     => 'string',
+				'default'  => '',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_formula' ],
+			],
+			'_pr_molecular_weight'      => [
+				'type'     => 'string',
+				'default'  => '',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_molecular_weight_string' ],
+			],
+			'_pr_aliases'               => [
+				'type'     => 'string',
+				'default'  => '[]',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_json_array' ],
+			],
+			// FAQ items (v0.6.0): [{question, answer}] JSON for FAQPage schema. Populated by CMO content sprint.
+			'_pr_faq_items'             => [
+				'type'     => 'string',
+				'default'  => '[]',
+				'sanitize' => [ PR_Core_Schema_Sanitizers::class, 'sanitize_faq_items' ],
+			],
 		];
 	}
 
@@ -160,12 +182,7 @@ class PR_Core_Peptide_CPT {
 	}
 
 	/**
-	 * Register the `peptide` custom post type.
+	 * Register the `peptide` CPT. Guarded with post_type_exists() so deploy order is irrelevant.
-	 *
-	 * Guarded with `post_type_exists()`: if another plugin (historically PSA)
-	 * has already registered the `peptide` post type, this call no-ops. This
-	 * makes deploy order between PR Core and PSA irrelevant during the
-	 * PSA v4.5.0 consolidation transition.
 	 *
 	 * Side effects: registers CPT with WordPress.
 	 *
@@ -218,15 +235,7 @@ class PR_Core_Peptide_CPT {
 	}
 
 	/**
-	 * Register the `peptide_category` taxonomy.
+	 * Register the `peptide_category` taxonomy. Guarded with taxonomy_exists().
-	 *
-	 * Guarded with `taxonomy_exists()` for the same reason CPT registration
-	 * is guarded. The 8 existing terms + term_relationships stay intact —
-	 * they key on taxonomy name `peptide_category` in wp_term_taxonomy,
-	 * which is exactly what we register here.
-	 *
-	 * v0.2.0: `pr_peptide_family` taxonomy removed — never populated, never
-	 * surfaced in UI.
 	 *
 	 * Side effects: registers taxonomy with WordPress.
 	 *
@@ -272,20 +281,6 @@ class PR_Core_Peptide_CPT {
 		}
 	}
 
-	/** Sanitize a JSON array string (e.g., aliases field). */
-	public static function sanitize_json_array( $value ): string {
-		if ( is_array( $value ) ) {
-			$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
-		}
-
-		$decoded = json_decode( (string) $value, true );
-		if ( ! is_array( $decoded ) ) {
-			return '[]';
-		}
-
-		return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
-	}
-
 	/** Sanitize evidence_strength to allowed enum values. */
 	public static function sanitize_evidence_strength( $value ): string {
 		$value = sanitize_text_field( (string) $value );

includes/cpt/class-pr-core-repo-daily-cpt.php

@@ -0,0 +1,80 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Registers the repo_daily custom post type for editorial publications.
+ *
+ * What: Defines the `repo_daily` CPT for articles, guides, comparisons, and news
+ *       generated by PRAutoBlogger and published under the Boo Sheeran byline.
+ * Who calls it: PR_Core::init() on plugins_loaded.
+ * Dependencies: None.
+ *
+ * Posts register at /daily/[slug]/ with title, editor, excerpt, thumbnail,
+ * and custom-fields support. REST-enabled for programmatic access by
+ * PRAutoBlogger and other integrations.
+ *
+ * @see ARCHITECTURE.md — Repo Daily type specification.
+ * @see CONVENTIONS.md — CPT ownership and extension patterns.
+ */
+class PR_Core_Repo_Daily_CPT {
+
+	/** @var string Post type slug (repo_daily). */
+	public const POST_TYPE = 'repo_daily';
+
+	/**
+	 * Register WordPress hooks for CPT registration.
+	 *
+	 * @return void
+	 */
+	public function register_hooks(): void {
+		add_action( 'init', [ __CLASS__, 'register_post_type' ] );
+	}
+
+	/**
+	 * Register the `repo_daily` custom post type.
+	 *
+	 * Side effects: registers CPT with WordPress.
+	 *
+	 * @return void
+	 */
+	public static function register_post_type(): void {
+		if ( post_type_exists( self::POST_TYPE ) ) {
+			return;
+		}
+
+		$labels = [
+			'name'               => __( 'Repo Daily', 'peptide-repo-core' ),
+			'singular_name'      => __( 'Repo Daily', 'peptide-repo-core' ),
+			'add_new_item'       => __( 'Add New Article', 'peptide-repo-core' ),
+			'edit_item'          => __( 'Edit Article', 'peptide-repo-core' ),
+			'new_item'           => __( 'New Article', 'peptide-repo-core' ),
+			'view_item'          => __( 'View Article', 'peptide-repo-core' ),
+			'search_items'       => __( 'Search Articles', 'peptide-repo-core' ),
+			'not_found'          => __( 'No articles found', 'peptide-repo-core' ),
+			'not_found_in_trash' => __( 'No articles found in trash', 'peptide-repo-core' ),
+			'all_items'          => __( 'All Articles', 'peptide-repo-core' ),
+			'menu_name'          => __( 'Repo Daily', 'peptide-repo-core' ),
+		];
+
+		$args = [
+			'labels'             => $labels,
+			'public'             => true,
+			'publicly_queryable' => true,
+			'show_ui'            => true,
+			'show_in_menu'       => true,
+			'show_in_nav_menus'  => true,
+			'show_in_rest'       => true,
+			'rest_base'          => 'repo_daily',
+			'menu_position'      => 6,
+			'menu_icon'          => 'dashicons-edit-page',
+			'capability_type'    => 'post',
+			'map_meta_cap'       => true,
+			'hierarchical'       => false,
+			'has_archive'        => true,
+			'rewrite'            => [ 'slug' => 'daily', 'with_front' => false ],
+			'supports'           => [ 'title', 'editor', 'excerpt', 'thumbnail', 'custom-fields' ],
+		];
+
+		register_post_type( self::POST_TYPE, $args );
+	}
+}

includes/cpt/class-pr-core-schema-sanitizers.php

@@ -0,0 +1,152 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Sanitizers for v0.6.0 schema-input meta fields.
+ *
+ * What: Static sanitizer methods for _pr_molecular_formula, _pr_molecular_weight,
+ *       and _pr_faq_items meta fields introduced in v0.6.0.
+ *
+ * Who calls it: PR_Core_Peptide_CPT::get_meta_fields() registers these as
+ *               sanitize_callback values for register_post_meta().
+ *
+ * Dependencies: WordPress sanitize_text_field, sanitize_textarea_field, wp_json_encode.
+ *
+ * @see cpt/class-pr-core-peptide-cpt.php — Meta field registration.
+ * @see ARCHITECTURE.md                   — §v0.6.0 schema sprint.
+ */
+class PR_Core_Schema_Sanitizers {
+
+	/**
+	 * Regex token for a single element symbol + optional count (e.g., "C10", "Na", "O").
+	 *
+	 * Matches: one uppercase letter, optionally followed by one lowercase letter,
+	 * optionally followed by one or more digits.
+	 *
+	 * @var string
+	 */
+	const FORMULA_TOKEN = '[A-Z][a-z]?\d*';
+
+	/**
+	 * Regex character class for allowed group-separator / structural characters.
+	 *
+	 * Covers: parentheses, square brackets, interpunct (·, U+00B7), period, digits.
+	 * These may appear between element tokens in complex or hydrated formulas.
+	 *
+	 * @var string
+	 */
+	const FORMULA_SEP = '[().\[\]\xB7\d]';
+
+	/**
+	 * Sanitize a molecular formula string (for _pr_molecular_formula).
+	 *
+	 * Strips HTML tags and control characters, then validates the value against
+	 * an element-formula grammar. Returns the longest leading run of valid
+	 * formula tokens and separators; returns '' when nothing valid is found.
+	 *
+	 * Grammar (per token): [A-Z][a-z]?\d* — an element symbol plus optional count.
+	 * Separators: ( ) [ ] · . and standalone digits (for hydrated formulas).
+	 * Input is treated as UNTRUSTED; downstream JSON escaping is unchanged.
+	 *
+	 * Examples:
+	 *   "C62H98N16O22"          → "C62H98N16O22"  (valid, unchanged)
+	 *   "C10H12\ninjection"     → "C10H12"         (injection stripped)
+	 *   "C2H5(OH)"              → "C2H5(OH)"       (parenthesised formula preserved)
+	 *   "<script>alert(1)</script>" → ""            (no valid leading token)
+	 *   ""                      → ""               (empty input)
+	 *
+	 * @param mixed $value Raw input value.
+	 * @return string Sanitized formula string, or '' when no valid formula found.
+	 */
+	public static function sanitize_molecular_formula( $value ): string {
+		// 1. Strip control characters (including newlines, tabs, null bytes).
+		$value = preg_replace( '/[\x00-\x1F\x7F]/', '', (string) $value ) ?? '';
+		// 2. Strip HTML tags; then strip remaining unsafe text characters.
+		$value = sanitize_text_field( wp_strip_all_tags( $value ) );
+		if ( '' === $value ) {
+			return '';
+		}
+		// 3. Extract the maximal leading run of valid element tokens and separators.
+		//    A valid run must start with an element token ([A-Z][a-z]?\d*), not a separator.
+		$pattern = '/^((?:' . self::FORMULA_TOKEN . '|' . self::FORMULA_SEP . ')+)/u';
+		if ( preg_match( $pattern, $value, $m ) ) {
+			return $m[1];
+		}
+		return '';
+	}
+
+	/**
+	 * Sanitize a molecular weight stored as a float string (for _pr_molecular_weight).
+	 *
+	 * Strips any trailing "Da" unit suffix, returns a float string.
+	 * Stored as string in post_meta to avoid float precision issues.
+	 * Returns empty string for invalid/zero inputs.
+	 *
+	 * @param mixed $value Raw input value (e.g., "1419.5" or "1419.5 Da").
+	 * @return string Float string (e.g., "1419.5"), or "" on invalid input.
+	 */
+	public static function sanitize_molecular_weight_string( $value ): string {
+		$clean = trim( preg_replace( '/\s*[Dd][Aa]\s*$/', '', trim( (string) $value ) ) ?? '' );
+		$f     = (float) $clean;
+		return $f > 0.0 ? (string) $f : '';
+	}
+
+	/**
+	 * Sanitize a JSON array string (e.g., for legacy aliases field or _pr_aliases).
+	 *
+	 * Accepts a JSON string or PHP array. Sanitizes each element individually.
+	 * Input is UNTRUSTED.
+	 *
+	 * @param mixed $value Raw input (JSON string or array).
+	 * @return string JSON array of sanitized strings, or '[]'.
+	 */
+	public static function sanitize_json_array( $value ): string {
+		if ( is_array( $value ) ) {
+			$value = wp_json_encode( array_map( 'sanitize_text_field', $value ) );
+		}
+
+		$decoded = json_decode( (string) $value, true );
+		if ( ! is_array( $decoded ) ) {
+			return '[]';
+		}
+
+		return wp_json_encode( array_values( array_map( 'sanitize_text_field', $decoded ) ) );
+	}
+
+	/**
+	 * Sanitize FAQ items JSON (for _pr_faq_items).
+	 *
+	 * Expects a JSON array of {question: string, answer: string} objects.
+	 * Sanitizes each question and answer individually.
+	 * Input is UNTRUSTED — malformed entries are silently dropped.
+	 *
+	 * @param mixed $value Raw input (JSON string or PHP array).
+	 * @return string JSON array of sanitized FAQ item objects, or '[]'.
+	 */
+	public static function sanitize_faq_items( $value ): string {
+		if ( is_string( $value ) ) {
+			$value = json_decode( $value, true );
+		}
+
+		if ( ! is_array( $value ) ) {
+			return '[]';
+		}
+
+		$clean = [];
+		foreach ( $value as $item ) {
+			if ( ! is_array( $item ) ) {
+				continue;
+			}
+			$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
+			$answer   = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
+			if ( '' !== $question && '' !== $answer ) {
+				$clean[] = [
+					'question' => $question,
+					'answer'   => $answer,
+				];
+			}
+		}
+
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+}

includes/frontend/class-pr-core-jsonld-drug.php

@@ -0,0 +1,158 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Builds the schema.org Drug graph piece for a peptide page.
+ *
+ * What: Assembles a Drug (+ MolecularEntity) schema node from peptide DTO
+ *       and the new _pr_* schema-input meta fields added in v0.6.0.
+ *
+ * Who calls it: PR_Core_Jsonld::build_drug_piece() during Yoast graph assembly
+ *               or standalone @graph construction.
+ *
+ * Dependencies: PR_Core_Peptide_DTO, WordPress get_post_meta(), get_permalink().
+ *
+ * @see frontend/class-pr-core-jsonld.php — Orchestrator that calls this builder.
+ * @see ARCHITECTURE.md                   — §2.7 JSON-LD output.
+ */
+class PR_Core_Jsonld_Drug {
+
+	/** @var string Meta key: molecular formula sourced by migration 0004. */
+	private const META_FORMULA  = '_pr_molecular_formula';
+
+	/** @var string Meta key: molecular weight (float string) sourced by migration 0004. */
+	private const META_WEIGHT   = '_pr_molecular_weight';
+
+	/** @var string Meta key: aliases JSON array sourced by migration 0004. */
+	private const META_ALIASES  = '_pr_aliases';
+
+	/** @var string Unit text for molecularWeight QuantitativeValue. */
+	private const UNIT_TEXT     = 'g/mol';
+
+	/**
+	 * Build a schema.org Drug piece array for a peptide.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return array<string, mixed> Schema.org Drug node.
+	 */
+	public function build( PR_Core_Peptide_DTO $peptide ): array {
+		$permalink = get_permalink( $peptide->id );
+
+		$node = [
+			'@type' => [ 'Drug', 'MolecularEntity' ],
+			'@id'   => $permalink . '#drug',
+			'name'  => $peptide->display_name ?: $peptide->title,
+			'url'   => $permalink,
+		];
+
+		if ( '' !== $peptide->excerpt ) {
+			$node['description'] = $peptide->excerpt;
+		}
+
+		// alternateName: prefer _pr_aliases (v0.6.0), fall back to DTO aliases field.
+		$aliases = $this->get_aliases( $peptide );
+		if ( ! empty( $aliases ) ) {
+			$node['alternateName'] = $aliases;
+		}
+
+		// molecularFormula: prefer _pr_molecular_formula, fall back to DTO field.
+		$formula = $this->get_formula( $peptide );
+		if ( '' !== $formula ) {
+			$node['molecularFormula'] = $formula;
+		}
+
+		// molecularWeight: prefer _pr_molecular_weight, fall back to DTO field.
+		$weight = $this->get_weight( $peptide );
+		if ( $weight > 0.0 ) {
+			$node['molecularWeight'] = [
+				'@type'    => 'QuantitativeValue',
+				'value'    => $weight,
+				'unitText' => self::UNIT_TEXT,
+			];
+		}
+
+		// External identifiers: CAS and DrugBank omitted in v0.6.0 (no source).
+		// @see ARCHITECTURE.md §v0.6.0 schema sprint — future enrichment.
+		$legal_status = $this->build_legal_status();
+		if ( null !== $legal_status ) {
+			$node['legalStatus'] = $legal_status;
+		}
+
+		/**
+		 * Filter the Drug schema node for a peptide.
+		 *
+		 * Known listeners: none.
+		 * Registered at: PR_Core::register_public_filters() — carried forward from v0.5.0.
+		 *
+		 * @param array<string, mixed> $node    Drug schema node.
+		 * @param PR_Core_Peptide_DTO  $peptide Peptide DTO.
+		 */
+		return apply_filters( 'pr_core_jsonld_peptide', $node, $peptide );
+	}
+
+	/**
+	 * Get aliases array from _pr_aliases meta, falling back to DTO aliases.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return string[] Sanitized alias strings.
+	 */
+	private function get_aliases( PR_Core_Peptide_DTO $peptide ): array {
+		$raw = get_post_meta( $peptide->id, self::META_ALIASES, true );
+
+		if ( is_string( $raw ) && '' !== $raw ) {
+			$decoded = json_decode( $raw, true );
+			if ( is_array( $decoded ) && ! empty( $decoded ) ) {
+				return array_values( array_filter( array_map( 'sanitize_text_field', $decoded ) ) );
+			}
+		}
+
+		// Fall back to DTO aliases (legacy bare-key meta).
+		return $peptide->aliases;
+	}
+
+	/**
+	 * Get molecular formula from _pr_molecular_formula meta, falling back to DTO.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return string Sanitized formula string, or '' if not available.
+	 */
+	private function get_formula( PR_Core_Peptide_DTO $peptide ): string {
+		$raw = (string) get_post_meta( $peptide->id, self::META_FORMULA, true );
+		if ( '' !== $raw ) {
+			return sanitize_text_field( $raw );
+		}
+		return $peptide->molecular_formula;
+	}
+
+	/**
+	 * Get molecular weight float from _pr_molecular_weight meta, falling back to DTO.
+	 *
+	 * @param PR_Core_Peptide_DTO $peptide Peptide DTO.
+	 * @return float Weight in g/mol, or 0.0 if not available.
+	 */
+	private function get_weight( PR_Core_Peptide_DTO $peptide ): float {
+		$raw = (string) get_post_meta( $peptide->id, self::META_WEIGHT, true );
+		if ( '' !== $raw ) {
+			$weight = (float) $raw;
+			if ( $weight > 0.0 ) {
+				return $weight;
+			}
+		}
+		return $peptide->molecular_weight;
+	}
+
+	/**
+	 * Build a standard legalStatus node for research compounds.
+	 *
+	 * Returns null when legalStatus should be omitted (future: when per-peptide
+	 * status is available from legal cells).
+	 *
+	 * @return array<string, string>|null
+	 */
+	private function build_legal_status(): ?array {
+		return [
+			'@type'       => 'DrugLegalStatus',
+			'description' => esc_html__( 'Not approved for human therapeutic use; supplied for laboratory research purposes only.', 'peptide-repo-core' ),
+		];
+	}
+}

includes/frontend/class-pr-core-jsonld-faq.php

@@ -0,0 +1,100 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Builds the schema.org FAQPage graph piece for a peptide page.
+ *
+ * What: Reads _pr_faq_items post-meta (JSON array of {question, answer} objects)
+ *       and produces a FAQPage node suitable for injection into Yoast's graph.
+ *       Emits nothing when the meta is empty or absent.
+ *
+ * Who calls it: PR_Core_Jsonld::build_faq_piece() during graph assembly.
+ * Dependencies: WordPress get_post_meta(), get_permalink().
+ *
+ * @see frontend/class-pr-core-jsonld.php       — Orchestrator that calls this builder.
+ * @see cpt/class-pr-core-schema-sanitizers.php — sanitize_faq_items() used on save.
+ * @see ARCHITECTURE.md                         — §2.7 JSON-LD output.
+ */
+class PR_Core_Jsonld_Faq {
+
+	/** @var string Meta key holding the FAQ items JSON array. */
+	public const META_FAQ_ITEMS = '_pr_faq_items';
+
+	/**
+	 * Build a FAQPage node for a post, or return null if no items exist.
+	 *
+	 * @param int    $post_id   WordPress post ID.
+	 * @param string $permalink Canonical permalink for @id construction.
+	 * @return array<string, mixed>|null FAQPage schema node, or null when no items.
+	 */
+	public function build( int $post_id, string $permalink ): ?array {
+		$items = $this->get_validated_items( $post_id );
+
+		if ( empty( $items ) ) {
+			return null;
+		}
+
+		return [
+			'@type'      => 'FAQPage',
+			'@id'        => $permalink . '#faq',
+			'mainEntity' => array_map( [ $this, 'build_question' ], $items ),
+		];
+	}
+
+	/**
+	 * Build a single Question node from a FAQ item array.
+	 *
+	 * @param array{question: string, answer: string} $item Sanitized FAQ item.
+	 * @return array<string, mixed> Schema.org Question node.
+	 */
+	private function build_question( array $item ): array {
+		return [
+			'@type' => 'Question',
+			'name'  => esc_html( $item['question'] ),
+			'acceptedAnswer' => [
+				'@type' => 'Answer',
+				'text'  => esc_html( $item['answer'] ),
+			],
+		];
+	}
+
+	/**
+	 * Read and validate _pr_faq_items meta, returning only well-formed items.
+	 *
+	 * Returns empty array when meta is absent, empty, or malformed.
+	 * Does not trust stored values — re-validates each item at read time.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return array<int, array{question: string, answer: string}> Validated items.
+	 */
+	private function get_validated_items( int $post_id ): array {
+		$raw = get_post_meta( $post_id, self::META_FAQ_ITEMS, true );
+
+		if ( ! is_string( $raw ) || '' === $raw ) {
+			return [];
+		}
+
+		$decoded = json_decode( $raw, true );
+
+		if ( ! is_array( $decoded ) || empty( $decoded ) ) {
+			return [];
+		}
+
+		$valid = [];
+		foreach ( $decoded as $item ) {
+			if ( ! is_array( $item ) ) {
+				continue;
+			}
+			$question = sanitize_text_field( (string) ( $item['question'] ?? '' ) );
+			$answer   = sanitize_textarea_field( (string) ( $item['answer'] ?? '' ) );
+			if ( '' !== $question && '' !== $answer ) {
+				$valid[] = [
+					'question' => $question,
+					'answer'   => $answer,
+				];
+			}
+		}
+
+		return $valid;
+	}
+}

includes/frontend/class-pr-core-jsonld-webpage.php

@@ -0,0 +1,145 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Enriches Yoast's WebPage node to MedicalWebPage for peptide single pages.
+ *
+ * What: Hooks into Yoast's wpseo_schema_webpage_type filter to retype the page
+ *       node to MedicalWebPage, and into wpseo_schema_graph to inject
+ *       lastReviewed, reviewedBy, and audience enrichments.
+ *
+ * Who calls it: PR_Core_Jsonld::register_hooks() registers both filters.
+ * Dependencies: Yoast SEO (wordpress-seo) ≥ 27.6 when active; graceful no-op otherwise.
+ *
+ * @see frontend/class-pr-core-jsonld.php — Parent orchestrator.
+ * @see ARCHITECTURE.md                   — §2.7 JSON-LD output, Yoast integration contract.
+ */
+class PR_Core_Jsonld_Webpage {
+
+	/** @var string Meta key for last editorial review date (ISO date string). */
+	private const META_LAST_REVIEWED = '_pr_last_reviewed';
+
+	/** @var string Meta key for last source verification date (ISO date string). */
+	private const META_LAST_VERIFIED = '_pr_last_source_verified';
+
+	/**
+	 * Return 'MedicalWebPage' as the schema type for peptide single pages.
+	 *
+	 * Hooked on: wpseo_schema_webpage_type (Yoast SEO ≥ 19.x).
+	 * Passes through unchanged on non-peptide pages.
+	 *
+	 * Yoast contract: passes a plain string (e.g., 'CollectionPage') for
+	 * non-singular special types, but an ARRAY (e.g., ['WebPage']) for every
+	 * singular page — including plain Pages and monographs. Under strict_types=1
+	 * a string-only signature throws TypeError on all singulars. This method
+	 * therefore accepts string|array and returns the same union type so callers
+	 * (Yoast's filter chain) receive the value in the shape they passed it.
+	 *
+	 * @param string|array $type Existing Yoast page type — string or string[].
+	 * @return string|array 'MedicalWebPage' (string) on peptide singles; $type unchanged otherwise.
+	 */
+	public function retype_to_medical_webpage( string|array $type ): string|array {
+		if ( is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return 'MedicalWebPage';
+		}
+		return $type;
+	}
+
+	/**
+	 * Enrich Yoast's graph pieces array for peptide single pages.
+	 *
+	 * Injects lastReviewed, reviewedBy, and audience into the WebPage/MedicalWebPage
+	 * node already in Yoast's graph. Does NOT add new WebPage or BreadcrumbList nodes.
+	 *
+	 * Hooked on: wpseo_schema_graph (Yoast SEO ≥ 19.x), priority 11.
+	 *
+	 * @param array<int, array<string, mixed>> $graph  Yoast schema graph pieces array.
+	 * @param \WPSEO_Schema_Context            $context Yoast schema context object.
+	 * @return array<int, array<string, mixed>> Modified graph.
+	 */
+	public function enrich_webpage_piece( array $graph, $context ): array {
+		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return $graph;
+		}
+
+		$post_id     = get_the_ID();
+		$enrichments = $this->build_webpage_enrichments( (int) $post_id );
+
+		if ( empty( $enrichments ) ) {
+			return $graph;
+		}
+
+		foreach ( $graph as &$piece ) {
+			if ( ! is_array( $piece ) ) {
+				continue;
+			}
+
+			// Yoast may set @type as a plain string OR an array of strings.
+			// Normalise to array so in_array() works regardless of shape.
+			$raw_type = $piece['@type'] ?? '';
+			$types    = is_array( $raw_type ) ? $raw_type : [ $raw_type ];
+
+			if ( in_array( 'WebPage', $types, true ) || in_array( 'MedicalWebPage', $types, true ) ) {
+				foreach ( $enrichments as $key => $value ) {
+					$piece[ $key ] = $value;
+				}
+				break;
+			}
+		}
+
+		return $graph;
+	}
+
+	/**
+	 * Build MedicalWebPage enrichment fields for a peptide post.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return array<string, mixed> Enrichment fields to merge into the WebPage node.
+	 */
+	private function build_webpage_enrichments( int $post_id ): array {
+		$enrichments = [];
+
+		// lastReviewed: prefer _pr_last_reviewed, fall back to _pr_last_source_verified,
+		// then post modified date.
+		$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_REVIEWED, true );
+		if ( '' === $last_reviewed ) {
+			$last_reviewed = (string) get_post_meta( $post_id, self::META_LAST_VERIFIED, true );
+		}
+		if ( '' === $last_reviewed ) {
+			$last_reviewed = get_post_modified_time( 'Y-m-d', false, $post_id ) ?: '';
+		}
+
+		if ( '' !== $last_reviewed ) {
+			$enrichments['lastReviewed'] = sanitize_text_field( $last_reviewed );
+		}
+
+		// reviewedBy: Person only when a medical editor is assigned; otherwise Organization.
+		$editor_id = (int) get_post_meta( $post_id, 'medical_editor_id', true );
+		if ( $editor_id > 0 ) {
+			$editor = get_userdata( $editor_id );
+			if ( $editor ) {
+				$enrichments['reviewedBy'] = [
+					'@type' => 'Person',
+					'name'  => sanitize_text_field( $editor->display_name ),
+					'url'   => get_author_posts_url( $editor_id ),
+				];
+			}
+		}
+
+		if ( ! isset( $enrichments['reviewedBy'] ) ) {
+			$enrichments['reviewedBy'] = [
+				'@type' => 'Organization',
+				'name'  => 'Peptide Repo',
+				'url'   => home_url(),
+			];
+		}
+
+		// audience: MedicalAudience for researchers.
+		$enrichments['audience'] = [
+			'@type'        => 'MedicalAudience',
+			'audienceType' => 'Researcher',
+		];
+
+		return $enrichments;
+	}
+}

includes/frontend/class-pr-core-jsonld.php

@@ -4,33 +4,137 @@ declare(strict_types=1);
 /**
  * JSON-LD / schema.org structured data emission for peptide pages.
  *
- * What: Emits Drug schema on single peptide pages, Dataset schema on archives.
+ * What: Integrates Drug, MedicalWebPage, and FAQPage schema into Yoast's graph
- * Who calls it: PR_Core::init() registers wp_head hook.
+ *       on single peptide pages. When Yoast is inactive, emits a standalone
- * Dependencies: PR_Core_Peptide_Repository for data lookup.
+ *       @graph block via wp_head as a fallback.
  *
- * Consumer plugins can override via pr_core_jsonld_peptide filter.
+ * Who calls it: PR_Core::init() calls register_hooks(). Yoast hooks fire on
+ *               every frontend page that Yoast processes.
  *
- * @see ARCHITECTURE.md — Section 2.7 JSON-LD output.
+ * Dependencies:
+ *   - Yoast SEO (wordpress-seo) ≥ 27.6 for integrated emission path.
+ *   - PR_Core_Jsonld_Drug, PR_Core_Jsonld_Webpage, PR_Core_Jsonld_Faq (builders).
+ *   - PR_Core_Peptide_Repository, PR_Core_Peptide_CPT (data).
+ *
+ * Yoast integration contract (ratified 2026-06-13, v0.6.2):
+ *   - wpseo_schema_graph_pieces delivers OBJECTS (Abstract_Schema_Piece subclasses)
+ *     to Yoast, which calls get_class() + is_needed() on every item. Injecting plain
+ *     arrays there causes a PHP Fatal. Drug/FAQ nodes must be injected via
+ *     wpseo_schema_graph instead, which receives the fully-assembled graph as
+ *     array-of-arrays and is safe for plain array appends.
+ *   - wpseo_schema_graph_pieces is therefore left UNHOOKED by this plugin.
+ *   - Integrated path: Yoast owns WebPage and BreadcrumbList — we never duplicate.
+ *   - Standalone fallback: emits a complete @graph (Drug + FAQPage) only.
+ *   - Drug @id: {permalink}#drug (stable for cross-plugin linking).
+ *
+ * @see frontend/class-pr-core-jsonld-drug.php    — Drug piece builder.
+ * @see frontend/class-pr-core-jsonld-webpage.php — MedicalWebPage enrichment.
+ * @see frontend/class-pr-core-jsonld-faq.php     — FAQPage piece builder.
+ * @see ARCHITECTURE.md                           — §2.7 JSON-LD output.
  */
 class PR_Core_Jsonld {
 
+	/** @var PR_Core_Jsonld_Drug Drug piece builder. */
+	private PR_Core_Jsonld_Drug $drug_builder;
+
+	/** @var PR_Core_Jsonld_Webpage MedicalWebPage enricher. */
+	private PR_Core_Jsonld_Webpage $webpage_enricher;
+
+	/** @var PR_Core_Jsonld_Faq FAQ piece builder. */
+	private PR_Core_Jsonld_Faq $faq_builder;
+
+	/**
+	 * Construct the orchestrator with its piece builders.
+	 */
+	public function __construct() {
+		$this->drug_builder     = new PR_Core_Jsonld_Drug();
+		$this->webpage_enricher = new PR_Core_Jsonld_Webpage();
+		$this->faq_builder      = new PR_Core_Jsonld_Faq();
+	}
+
 	/**
 	 * Register hooks for JSON-LD output.
 	 *
+	 * Registers the Yoast-integrated path via wpseo_schema_graph (safe for plain
+	 * array appends) and the standalone wp_head fallback (active only when Yoast
+	 * is absent). Does NOT hook wpseo_schema_graph_pieces — Yoast calls
+	 * get_class() + is_needed() on every item in that filter's array and will
+	 * fatal on a plain PHP array (see class-level docblock).
+	 *
+	 * Side effects: calls add_filter(), add_action().
+	 *
 	 * @return void
 	 */
 	public function register_hooks(): void {
-		add_action( 'wp_head', [ $this, 'emit_jsonld' ], 99 );
+		// wpseo_schema_webpage_type: retype WebPage -> MedicalWebPage on peptide singles.
+		add_filter( 'wpseo_schema_webpage_type', [ $this->webpage_enricher, 'retype_to_medical_webpage' ] );
+
+		// wpseo_schema_graph: two callbacks at different priorities.
+		// Priority 11 -- enrich_webpage_piece: merge lastReviewed/reviewedBy/audience into the
+		//               existing WebPage node that Yoast already emitted.
+		// Priority 12 -- inject_graph_nodes: append Drug + FAQPage arrays to the graph.
+		//               Must run after enrich_webpage_piece so the WebPage node is already
+		//               enriched before Drug/FAQ are appended.
+		add_filter( 'wpseo_schema_graph', [ $this->webpage_enricher, 'enrich_webpage_piece' ], 11, 2 );
+		add_filter( 'wpseo_schema_graph', [ $this, 'inject_graph_nodes' ], 12, 2 );
+
+		// Standalone fallback: emits only when Yoast is not producing output.
+		add_action( 'wp_head', [ $this, 'emit_standalone_fallback' ], 99 );
 	}
 
 	/**
-	 * Emit JSON-LD on peptide single pages.
+	 * Append Drug and FAQPage nodes to Yoast's fully-assembled schema graph.
 	 *
-	 * Side effects: outputs script tag in wp_head.
+	 * Hooked on: wpseo_schema_graph (priority 12, after enrich_webpage_piece).
+	 * This filter receives Yoast's completed graph as an array of plain arrays.
+	 * Appending plain Drug/FAQ arrays here is safe -- unlike wpseo_schema_graph_pieces
+	 * which calls get_class() and is_needed() on each item expecting objects.
+	 *
+	 * @param array<int, array<string, mixed>>                        $graph   Assembled Yoast graph.
+	 * @param \Yoast\WP\SEO\Context\Meta_Tags_Context|null            $context Yoast schema context.
+	 * @return array<int, array<string, mixed>> Graph with Drug (and optionally FAQ) appended.
+	 */
+	public function inject_graph_nodes( array $graph, $context ): array {
+		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
+			return $graph;
+		}
+
+		$post_id = get_the_ID();
+		if ( ! $post_id ) {
+			return $graph;
+		}
+
+		$peptide = ( new PR_Core_Peptide_Repository() )->find_by_id( (int) $post_id );
+		if ( ! $peptide ) {
+			return $graph;
+		}
+
+		$graph[] = $this->drug_builder->build( $peptide );
+
+		$faq_node = $this->faq_builder->build( (int) $post_id, get_permalink( (int) $post_id ) );
+		if ( null !== $faq_node ) {
+			$graph[] = $faq_node;
+		}
+
+		return $graph;
+	}
+
+	/**
+	 * Emit a standalone @graph block via wp_head when Yoast is not active.
+	 *
+	 * Guard: suppressed if Yoast is loaded (function_exists check). This is the
+	 * no-Yoast fallback required by the jsonld-contract. When Yoast is present,
+	 * the integrated path (inject_graph_nodes via wpseo_schema_graph) handles emission.
+	 *
+	 * Side effects: outputs a script tag in wp_head.
 	 *
 	 * @return void
 	 */
-	public function emit_jsonld(): void {
+	public function emit_standalone_fallback(): void {
+		if ( function_exists( 'YoastSEO' ) ) {
+			return;
+		}
+
 		if ( ! is_singular( PR_Core_Peptide_CPT::POST_TYPE ) ) {
 			return;
 		}
@@ -40,86 +144,25 @@ class PR_Core_Jsonld {
 			return;
 		}
 
-		$repo    = new PR_Core_Peptide_Repository();
+		$peptide = ( new PR_Core_Peptide_Repository() )->find_by_id( (int) $post_id );
-		$peptide = $repo->find_by_id( $post_id );
-
 		if ( ! $peptide ) {
 			return;
 		}
 
-		$schema = $this->build_drug_schema( $peptide );
+		$permalink = get_permalink( (int) $post_id );
+		$graph     = [ $this->drug_builder->build( $peptide ) ];
 
-		/**
+		$faq_node = $this->faq_builder->build( (int) $post_id, $permalink );
-		 * Filter the JSON-LD schema for a peptide page.
+		if ( null !== $faq_node ) {
-		 *
+			$graph[] = $faq_node;
-		 * @param array<string, mixed>  $schema  Schema.org data array.
-		 * @param PR_Core_Peptide_DTO   $peptide The peptide DTO.
-		 */
-		$schema = apply_filters( 'pr_core_jsonld_peptide', $schema, $peptide );
-
-		if ( empty( $schema ) ) {
-			return;
 		}
 
 		printf(
 			'<script type="application/ld+json">%s</script>' . "\n",
-			wp_json_encode( $schema, JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT )
+			wp_json_encode(
+				[ '@context' => 'https://schema.org', '@graph' => $graph ],
+				JSON_UNESCAPED_SLASHES | JSON_UNESCAPED_UNICODE | JSON_PRETTY_PRINT
+			)
 		);
 	}
-
-	/**
-	 * Build a schema.org Drug object for a peptide.
-	 *
-	 * @param PR_Core_Peptide_DTO $peptide Peptide data.
-	 * @return array<string, mixed> Schema.org JSON-LD structure.
-	 */
-	private function build_drug_schema( PR_Core_Peptide_DTO $peptide ): array {
-		$schema = [
-			'@context'         => 'https://schema.org',
-			'@type'            => 'Drug',
-			'name'             => $peptide->display_name ?: $peptide->title,
-			'url'              => get_permalink( $peptide->id ),
-			'description'      => $peptide->excerpt,
-		];
-
-		if ( ! empty( $peptide->aliases ) ) {
-			$schema['alternateName'] = $peptide->aliases;
-		}
-
-		if ( '' !== $peptide->molecular_formula ) {
-			$schema['molecularFormula'] = $peptide->molecular_formula;
-		}
-
-		if ( $peptide->molecular_weight > 0 ) {
-			$schema['molecularWeight'] = [
-				'@type'    => 'QuantitativeValue',
-				'value'    => $peptide->molecular_weight,
-				'unitText' => 'Da',
-			];
-		}
-
-		// External identifiers as codes.
-		$codes = [];
-		if ( '' !== $peptide->cas_number ) {
-			$codes[] = [
-				'@type'       => 'MedicalCode',
-				'codeValue'   => $peptide->cas_number,
-				'codingSystem' => 'CAS',
-			];
-		}
-
-		if ( '' !== $peptide->drugbank_id ) {
-			$codes[] = [
-				'@type'       => 'MedicalCode',
-				'codeValue'   => $peptide->drugbank_id,
-				'codingSystem' => 'DrugBank',
-			];
-		}
-
-		if ( ! empty( $codes ) ) {
-			$schema['code'] = $codes;
-		}
-
-		return $schema;
-	}
 }

includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php

@@ -0,0 +1,270 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Migration 0004: Backfill peptide schema meta from PSA psa_* keys.
+ *
+ * What: Copies PSA-stored PubChem data (molecular formula, weight, aliases)
+ *       into PR Core's own _pr_molecular_formula, _pr_molecular_weight,
+ *       _pr_aliases meta keys on all published peptide posts.
+ *       For posts missing PSA data, attempts a PubChem REST lookup via
+ *       PR_Core_Pubchem_Client.
+ *
+ * Who calls it: PR_Core_Migration_Runner::run_pending().
+ * Dependencies: WordPress get_post_meta(), update_post_meta(), get_posts().
+ *               PR_Core_Pubchem_Client for PubChem fallback.
+ *               PR_Core_Schema_Sanitizers for formula sanitization.
+ *               PR_Core_Peptide_CPT::POST_TYPE for query.
+ *
+ * Idempotent: skips posts where all three PR Core meta keys are already non-empty.
+ * Re-runnable: safe to run multiple times.
+ *
+ * PSA source keys (all treated as UNTRUSTED — sanitized before writing):
+ *   psa_molecular_formula  => _pr_molecular_formula  (string)
+ *   psa_molecular_weight   => _pr_molecular_weight   (float string, strip "Da")
+ *   psa_aliases            => _pr_aliases            (JSON array string)
+ *
+ * @see ARCHITECTURE.md     — §v0.6.0 schema sprint.
+ * @see CONVENTIONS.md      — How To: Add a New Migration.
+ * @see class-pr-core-pubchem-client.php — HTTP client for PubChem REST.
+ */
+class PR_Core_Migration_0004_Backfill_Peptide_Meta {
+
+	/** @var string Meta key: molecular formula (PR Core namespace). */
+	public const META_FORMULA = '_pr_molecular_formula';
+
+	/** @var string Meta key: molecular weight as float string (PR Core namespace). */
+	public const META_WEIGHT  = '_pr_molecular_weight';
+
+	/** @var string Meta key: aliases JSON array (PR Core namespace). */
+	public const META_ALIASES = '_pr_aliases';
+
+	/** @var PR_Core_Pubchem_Client HTTP client for PubChem REST API. */
+	private PR_Core_Pubchem_Client $pubchem;
+
+	/**
+	 * Construct migration with optional PubChem client (injectable for testing).
+	 *
+	 * @param PR_Core_Pubchem_Client|null $pubchem PubChem client; creates default if null.
+	 */
+	public function __construct( ?PR_Core_Pubchem_Client $pubchem = null ) {
+		$this->pubchem = $pubchem ?? new PR_Core_Pubchem_Client();
+	}
+
+	/**
+	 * Run the backfill migration.
+	 *
+	 * Side effects: reads post meta, writes post meta, logs via error_log.
+	 *
+	 * @return void
+	 */
+	public function up(): void {
+		$peptide_ids = $this->get_all_peptide_ids();
+
+		if ( empty( $peptide_ids ) ) {
+			error_log( '[PR Core Migration 0004] No peptide posts found — nothing to backfill.' );
+			return;
+		}
+
+		$counts = [ 'skipped' => 0, 'copied_psa' => 0, 'pubchem_ok' => 0, 'pubchem_skip' => 0 ];
+
+		foreach ( $peptide_ids as $post_id ) {
+			$result             = $this->backfill_post( $post_id );
+			$counts[ $result ] += 1;
+		}
+
+		error_log( sprintf(
+			'[PR Core Migration 0004] Complete. Skipped: %d, PSA-copied: %d, PubChem-ok: %d, PubChem-skip: %d',
+			$counts['skipped'],
+			$counts['copied_psa'],
+			$counts['pubchem_ok'],
+			$counts['pubchem_skip']
+		) );
+	}
+
+	/**
+	 * Backfill meta for a single peptide post.
+	 *
+	 * @param int $post_id WordPress post ID.
+	 * @return string Result: skipped|copied_psa|pubchem_ok|pubchem_skip.
+	 */
+	private function backfill_post( int $post_id ): string {
+		$existing_formula = (string) get_post_meta( $post_id, self::META_FORMULA, true );
+		$existing_weight  = (string) get_post_meta( $post_id, self::META_WEIGHT, true );
+		$existing_aliases = (string) get_post_meta( $post_id, self::META_ALIASES, true );
+
+		// Idempotency limitation: this guard is all-or-nothing. A peptide that legitimately
+		// has no aliases (e.g., a novel compound) will never satisfy all three conditions and
+		// the migration will re-run on every manual re-invoke. This is safe because
+		// write_meta_from_psa() / write_meta_from_pubchem() only overwrite with non-empty
+		// values, but callers should be aware the 'skipped' result requires all three keys set.
+		if ( '' !== $existing_formula && '' !== $existing_weight && '' !== $existing_aliases ) {
+			return 'skipped';
+		}
+
+		$psa_formula = (string) get_post_meta( $post_id, 'psa_molecular_formula', true );
+
+		if ( '' !== $psa_formula ) {
+			$psa_weight  = (string) get_post_meta( $post_id, 'psa_molecular_weight', true );
+			$psa_aliases = (string) get_post_meta( $post_id, 'psa_aliases', true );
+			$this->write_meta_from_psa( $post_id, $psa_formula, $psa_weight, $psa_aliases );
+			return 'copied_psa';
+		}
+
+		// No PSA data — attempt PubChem REST lookup.
+		$psa_cid = (string) get_post_meta( $post_id, 'psa_pubchem_cid', true );
+		$post    = get_post( $post_id );
+		$name    = $post ? sanitize_text_field( $post->post_title ) : '';
+
+		$data = ( '' !== $psa_cid && ctype_digit( $psa_cid ) )
+			? $this->pubchem->fetch_by_cid( $psa_cid )
+			: null;
+
+		if ( null === $data && '' !== $name ) {
+			$data = $this->pubchem->fetch_by_name( $name );
+		}
+
+		if ( null === $data ) {
+			error_log( sprintf(
+				'[PR Core Migration 0004] Post ID %d (%s): PubChem returned no data — leaving meta empty.',
+				$post_id,
+				esc_html( $name )
+			) );
+			return 'pubchem_skip';
+		}
+
+		$formula      = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $data['formula'] );
+		$weight       = (float) $data['weight'];
+		$aliases_json = $this->synonyms_to_json( $data['synonyms'] ?? [] );
+		$this->write_pr_meta( $post_id, $formula, $weight, $aliases_json );
+
+		error_log( sprintf(
+			'[PR Core Migration 0004] Post ID %d (%s): PubChem-sourced formula=%s weight=%s',
+			$post_id,
+			esc_html( $name ),
+			$formula,
+			(string) $weight
+		) );
+
+		return 'pubchem_ok';
+	}
+
+	/**
+	 * Write PR Core meta from PSA source values.
+	 *
+	 * Input is UNTRUSTED — sanitizes before writing.
+	 *
+	 * @param int    $post_id  WordPress post ID.
+	 * @param string $formula  Raw psa_molecular_formula value.
+	 * @param string $weight   Raw psa_molecular_weight value (may include " Da").
+	 * @param string $aliases  Raw psa_aliases value (comma-separated).
+	 * @return void
+	 */
+	private function write_meta_from_psa( int $post_id, string $formula, string $weight, string $aliases ): void {
+		$clean_formula = PR_Core_Schema_Sanitizers::sanitize_molecular_formula( $formula );
+		$clean_weight  = $this->parse_weight( $weight );
+		$clean_aliases = $this->parse_aliases_string( $aliases );
+		$this->write_pr_meta( $post_id, $clean_formula, $clean_weight, $clean_aliases );
+	}
+
+	/**
+	 * Write the three PR Core meta keys for a post.
+	 *
+	 * Only writes a field when it has a usable value to avoid overwriting
+	 * existing data with empty placeholders.
+	 *
+	 * @param int    $post_id  WordPress post ID.
+	 * @param string $formula  Sanitized formula (empty = skip).
+	 * @param float  $weight   Parsed weight in g/mol (0 = skip).
+	 * @param string $aliases  JSON array string (empty array = skip).
+	 * @return void
+	 */
+	private function write_pr_meta( int $post_id, string $formula, float $weight, string $aliases ): void {
+		if ( '' !== $formula ) {
+			update_post_meta( $post_id, self::META_FORMULA, $formula );
+		}
+
+		if ( $weight > 0.0 ) {
+			update_post_meta( $post_id, self::META_WEIGHT, (string) $weight );
+		} elseif ( '' !== $formula ) {
+			error_log( '[PR Core Migration 0004] Post ID ' . $post_id . ': weight parsed to 0 — check source.' );
+		}
+
+		$decoded = json_decode( $aliases, true );
+		if ( is_array( $decoded ) && count( $decoded ) > 0 ) {
+			update_post_meta( $post_id, self::META_ALIASES, $aliases );
+		}
+	}
+
+	/**
+	 * Parse a molecular weight string to a float.
+	 *
+	 * Strips trailing " Da" suffix (case-insensitive) and whitespace.
+	 * Returns 0.0 on parse failure.
+	 *
+	 * @param string $value Raw weight value (e.g., "1419.5 Da").
+	 * @return float Parsed weight in g/mol, 0.0 on failure.
+	 */
+	public function parse_weight( string $value ): float {
+		$clean = trim( preg_replace( '/\s*[Dd][Aa]\s*$/', '', trim( $value ) ) ?? '' );
+		return (float) $clean;
+	}
+
+	/**
+	 * Parse a comma-separated alias string into a sanitized JSON array string.
+	 *
+	 * Input is UNTRUSTED — each alias is sanitized individually.
+	 *
+	 * @param string $value Comma-separated aliases.
+	 * @return string JSON array of sanitized strings, or '[]' if empty.
+	 */
+	public function parse_aliases_string( string $value ): string {
+		if ( '' === trim( $value ) ) {
+			return '[]';
+		}
+
+		$clean = [];
+		foreach ( explode( ',', $value ) as $part ) {
+			$alias = sanitize_text_field( trim( $part ) );
+			if ( '' !== $alias ) {
+				$clean[] = $alias;
+			}
+		}
+
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+
+	/**
+	 * Convert a raw synonyms array from PubChem to a JSON string.
+	 *
+	 * Sanitizes each synonym. Returns '[]' on empty input.
+	 *
+	 * @param string[] $synonyms Raw synonym strings from PubChem.
+	 * @return string JSON array of sanitized strings.
+	 */
+	private function synonyms_to_json( array $synonyms ): string {
+		$clean = [];
+		foreach ( $synonyms as $syn ) {
+			$alias = sanitize_text_field( (string) $syn );
+			if ( '' !== $alias ) {
+				$clean[] = $alias;
+			}
+		}
+		return wp_json_encode( $clean, JSON_UNESCAPED_UNICODE ) ?: '[]';
+	}
+
+	/**
+	 * Get IDs of all published peptide posts.
+	 *
+	 * @return int[]
+	 */
+	private function get_all_peptide_ids(): array {
+		$posts = get_posts( [
+			'post_type'      => PR_Core_Peptide_CPT::POST_TYPE,
+			'post_status'    => 'publish',
+			'posts_per_page' => -1,
+			'fields'         => 'ids',
+		] );
+		return array_map( 'intval', is_array( $posts ) ? $posts : [] );
+	}
+}

includes/migrations/class-pr-core-migration-runner.php

@@ -29,6 +29,7 @@ class PR_Core_Migration_Runner {
 		'PR_Core_Migration_0001_Dosing_Rows',
 		'PR_Core_Migration_0002_Legal_Cells',
 		'PR_Core_Migration_0003_Candidate_Queue',
+		'PR_Core_Migration_0004_Backfill_Peptide_Meta',
 	];
 
 	/**

includes/migrations/class-pr-core-pubchem-client.php

@@ -0,0 +1,208 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Lightweight PubChem REST client for the backfill migration.
+ *
+ * What: Fetches molecular formula, molecular weight, and synonyms from the
+ *       PubChem REST API for a given compound CID or name. Used exclusively
+ *       by migration 0004 for the 4 peptide posts that lack PSA-sourced data.
+ *
+ * Who calls it: PR_Core_Migration_0004_Backfill_Peptide_Meta::fetch_pubchem().
+ * Dependencies: WordPress wp_remote_get() when available; falls back to
+ *               file_get_contents with stream context (WP-CLI context).
+ *
+ * All values from PubChem are returned unsanitized — callers must sanitize
+ * before writing to post_meta.
+ *
+ * @see migrations/class-pr-core-migration-0004-backfill-peptide-meta.php — Caller.
+ * @see ARCHITECTURE.md — §v0.6.0 schema sprint.
+ */
+class PR_Core_Pubchem_Client {
+
+	/** @var string PubChem REST base URL. */
+	private const BASE = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug';
+
+	/** @var int HTTP timeout per request (seconds). */
+	private const TIMEOUT = 8;
+
+	/** @var int Maximum retry attempts with exponential backoff. */
+	private const MAX_RETRIES = 3;
+
+	/** @var int Maximum synonyms to return (keeps post-meta size reasonable). */
+	private const MAX_SYNONYMS = 10;
+
+	/**
+	 * Fetch properties and synonyms by PubChem CID.
+	 *
+	 * @param string $cid Numeric PubChem CID string.
+	 * @return array{formula: string, weight: float, synonyms: string[]}|null Null on failure.
+	 */
+	public function fetch_by_cid( string $cid ): ?array {
+		if ( '' === $cid || ! ctype_digit( $cid ) ) {
+			return null;
+		}
+
+		$props = $this->fetch_properties( 'cid', $cid );
+		if ( null === $props ) {
+			return null;
+		}
+
+		$props['synonyms'] = $this->fetch_synonyms( 'cid', $cid );
+		return $props;
+	}
+
+	/**
+	 * Fetch properties and synonyms by compound name.
+	 *
+	 * @param string $name Compound name (e.g., peptide post title).
+	 * @return array{formula: string, weight: float, synonyms: string[]}|null Null on failure.
+	 */
+	public function fetch_by_name( string $name ): ?array {
+		if ( '' === trim( $name ) ) {
+			return null;
+		}
+
+		$props = $this->fetch_properties( 'name', $name );
+		if ( null === $props ) {
+			return null;
+		}
+
+		// If a CID was returned in the property response, use it for synonyms (more reliable).
+		$cid  = $props['cid'] ?? '';
+		$type = ( '' !== $cid ) ? 'cid' : 'name';
+		$ref  = ( '' !== $cid ) ? $cid : $name;
+
+		$props['synonyms'] = $this->fetch_synonyms( $type, $ref );
+		unset( $props['cid'] );
+		return $props;
+	}
+
+	/**
+	 * Fetch MolecularFormula and MolecularWeight from PubChem.
+	 *
+	 * @param string $lookup_type 'cid' or 'name'.
+	 * @param string $identifier  CID number or compound name.
+	 * @return array{formula: string, weight: float, cid: string}|null
+	 */
+	private function fetch_properties( string $lookup_type, string $identifier ): ?array {
+		$url  = self::BASE . '/compound/' . $lookup_type . '/' . rawurlencode( $identifier )
+			. '/property/MolecularFormula,MolecularWeight/JSON';
+		$body = $this->get_with_retry( $url );
+
+		if ( null === $body ) {
+			return null;
+		}
+
+		$data  = json_decode( $body, true );
+		$props = $data['PropertyTable']['Properties'][0] ?? null;
+
+		if ( ! is_array( $props ) ) {
+			return null;
+		}
+
+		$formula = (string) ( $props['MolecularFormula'] ?? '' );
+		$weight  = (float) ( $props['MolecularWeight'] ?? 0 );
+		$cid     = (string) ( $props['CID'] ?? '' );
+
+		if ( '' === $formula || $weight <= 0.0 ) {
+			return null;
+		}
+
+		return [
+			'formula' => $formula,
+			'weight'  => $weight,
+			'cid'     => $cid,
+		];
+	}
+
+	/**
+	 * Fetch synonyms for a compound, limited to MAX_SYNONYMS.
+	 *
+	 * Returns an empty array on failure — callers treat this gracefully.
+	 *
+	 * @param string $lookup_type 'cid' or 'name'.
+	 * @param string $identifier  CID or name value.
+	 * @return string[] Raw synonym strings (unsanitized).
+	 */
+	private function fetch_synonyms( string $lookup_type, string $identifier ): array {
+		$url  = self::BASE . '/compound/' . $lookup_type . '/' . rawurlencode( $identifier ) . '/synonyms/JSON';
+		$body = $this->get_with_retry( $url );
+
+		if ( null === $body ) {
+			return [];
+		}
+
+		$data     = json_decode( $body, true );
+		$synonyms = $data['InformationList']['Information'][0]['Synonym'] ?? [];
+
+		if ( ! is_array( $synonyms ) ) {
+			return [];
+		}
+
+		return array_slice( $synonyms, 0, self::MAX_SYNONYMS );
+	}
+
+	/**
+	 * GET request with exponential-backoff retry (up to MAX_RETRIES).
+	 *
+	 * @param string $url URL to fetch.
+	 * @return string|null Response body on HTTP 200, null after all retries fail.
+	 */
+	private function get_with_retry( string $url ): ?string {
+		for ( $attempt = 0; $attempt < self::MAX_RETRIES; $attempt++ ) {
+			if ( $attempt > 0 ) {
+				sleep( (int) pow( 2, $attempt - 1 ) ); // 1s, 2s.
+			}
+
+			$body = $this->get_once( $url );
+			if ( null !== $body ) {
+				return $body;
+			}
+		}
+
+		error_log( '[PR Core PubChem] Request failed after ' . self::MAX_RETRIES . ' attempts: ' . $url );
+		return null;
+	}
+
+	/**
+	 * Single HTTP GET attempt.
+	 *
+	 * Uses wp_remote_get() when available; falls back to file_get_contents
+	 * for WP-CLI contexts where the HTTP API may not be bootstrapped.
+	 *
+	 * @param string $url URL to fetch.
+	 * @return string|null Body on HTTP 200, null on error or non-200.
+	 */
+	private function get_once( string $url ): ?string {
+		if ( function_exists( 'wp_remote_get' ) ) {
+			$response = wp_remote_get( $url, [
+				'timeout' => self::TIMEOUT,
+				'headers' => [ 'Accept' => 'application/json' ],
+			] );
+
+			if ( is_wp_error( $response ) ) {
+				return null;
+			}
+
+			if ( 200 !== (int) wp_remote_retrieve_response_code( $response ) ) {
+				return null;
+			}
+
+			$body = wp_remote_retrieve_body( $response );
+			return is_string( $body ) ? $body : null;
+		}
+
+		// WP-CLI / plain PHP fallback.
+		$context = stream_context_create( [
+			'http' => [
+				'timeout' => self::TIMEOUT,
+				'header'  => "Accept: application/json\r\n",
+				'method'  => 'GET',
+			],
+		] );
+
+		$body = @file_get_contents( $url, false, $context );
+		return ( false === $body ) ? null : $body;
+	}
+}

includes/taxonomies/class-pr-core-repo-daily-taxonomy.php

@@ -0,0 +1,78 @@
+<?php
+declare(strict_types=1);
+
+/**
+ * Registers the repo_daily_category taxonomy for Repo Daily articles.
+ *
+ * What: Defines the `repo_daily_category` taxonomy attached to repo_daily CPT.
+ *       Seeds four content categories on activation: article, guide, comparison, news.
+ * Who calls it: PR_Core::init() on plugins_loaded; activation hook seeding.
+ * Dependencies: None.
+ *
+ * Non-hierarchical taxonomy with REST support. Used by editorial and publishing
+ * workflows to categorize Repo Daily content.
+ *
+ * @see ARCHITECTURE.md — Content type taxonomy specification.
+ * @see CONVENTIONS.md — Taxonomy ownership pattern.
+ */
+class PR_Core_Repo_Daily_Taxonomy {
+
+	/** @var string Taxonomy: repo_daily_category. */
+	public const TAX_CATEGORY = 'repo_daily_category';
+
+	/**
+	 * Register WordPress hooks for taxonomy and seeding.
+	 *
+	 * @return void
+	 */
+	public function register_hooks(): void {
+		add_action( 'init', [ __CLASS__, 'register_taxonomy' ] );
+	}
+
+	/**
+	 * Register the `repo_daily_category` taxonomy.
+	 *
+	 * Side effects: registers taxonomy with WordPress.
+	 *
+	 * @return void
+	 */
+	public static function register_taxonomy(): void {
+		if ( taxonomy_exists( self::TAX_CATEGORY ) ) {
+			return;
+		}
+
+		register_taxonomy( self::TAX_CATEGORY, PR_Core_Repo_Daily_CPT::POST_TYPE, [
+			'labels'             => [
+				'name'          => __( 'Category', 'peptide-repo-core' ),
+				'singular_name' => __( 'Category', 'peptide-repo-core' ),
+			],
+			'public'             => true,
+			'publicly_queryable' => true,
+			'show_in_rest'       => true,
+			'show_ui'            => true,
+			'show_admin_column'  => true,
+			'hierarchical'       => false,
+			'rewrite'            => [ 'slug' => 'daily/category', 'with_front' => false ],
+		] );
+	}
+
+	/**
+	 * Seed default category terms on activation.
+	 *
+	 * Idempotent: checks for existence of each term before inserting.
+	 * Called by PR_Core_Activator during plugin activation.
+	 *
+	 * Side effects: may insert terms into wp_terms and wp_term_taxonomy.
+	 *
+	 * @return void
+	 */
+	public static function seed_terms(): void {
+		$terms = [ 'article', 'guide', 'comparison', 'news' ];
+
+		foreach ( $terms as $term ) {
+			if ( ! term_exists( $term, self::TAX_CATEGORY ) ) {
+				wp_insert_term( $term, self::TAX_CATEGORY );
+			}
+		}
+	}
+}

peptide-repo-core.php

@@ -3,7 +3,7 @@
  * Plugin Name: Peptide Repo Core
  * Plugin URI:  https://peptiderepo.com
  * Description: Canonical peptide schema — shared data layer for the peptiderepo.com ecosystem. Provides the peptide CPT, dosing rows, legal status cells, AI candidate queue, disclaimer component, and JSON-LD output.
- * Version:     0.4.0
+ * Version:     0.6.2
  * Author:      peptiderepo
  * Author URI:  https://peptiderepo.com
  * License:     GPL-2.0-or-later
@@ -22,11 +22,11 @@ if ( ! defined( 'ABSPATH' ) ) {
 
 /* ── Constants ────────────────────────────────────────────────────────── */
 
-define( 'PR_CORE_VERSION', '0.4.0' );
+define( 'PR_CORE_VERSION', '0.6.2' );
 define( 'PR_CORE_PLUGIN_FILE', __FILE__ );
 define( 'PR_CORE_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
 define( 'PR_CORE_PLUGIN_URL', plugin_dir_url( __FILE__ ) );
-define( 'PR_CORE_TARGET_SCHEMA_VERSION', 3 );
+define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
 
 /* ── Autoloader ───────────────────────────────────────────────────────── */
 

tests/bootstrap.php

@@ -113,8 +113,10 @@ function sanitize_text_field( $value ): string {
 	return is_scalar( $value ) ? trim( (string) $value ) : '';
 }
 
-function wp_json_encode( $data ): string {
+if ( ! function_exists( 'wp_json_encode' ) ) {
-	return json_encode( $data ) ?: '[]';
+	function wp_json_encode( $data, int $flags = 0 ): string {
+		return json_encode( $data, $flags ) ?: '[]';
+	}
 }
 
 function absint( $value ): int {

tests/unit/test-jsonld-peptide-piece.php

@@ -0,0 +1,366 @@
+<?php
+/**
+ * Regression tests for v0.6.2: inject_graph_pieces (plain array) fatal on Yoast.
+ *
+ * Root cause: v0.6.0 and v0.6.1 hooked wpseo_schema_graph_pieces and appended
+ * plain PHP arrays (Drug, FAQ) to Yoast's pieces array. Yoast's
+ * Schema_Generator::filter_graph_pieces_to_generate() then called get_class()
+ * and is_needed() on every piece expecting objects extending Abstract_Schema_Piece.
+ * Passing a plain array caused:
+ *
+ *   PHP Fatal: get_class(): Argument #1 ($object) must be of type object, array given
+ *
+ * This crashed every peptide monograph page (HTTP 500) while /about/ and
+ * /peptides/ archive returned 200 (they don't enter the is_singular('peptide')
+ * branch).
+ *
+ * Fix: move Drug + FAQ injection to wpseo_schema_graph (priority 12) which
+ * receives the fully-assembled graph as an array of plain arrays — safe for
+ * plain array appends. wpseo_schema_graph_pieces is no longer hooked.
+ *
+ * These tests FAIL against v0.6.1 inject_graph_pieces and PASS after the
+ * v0.6.2 inject_graph_nodes fix.
+ *
+ * Run: php tests/unit/test-jsonld-peptide-piece.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs ─────────────────────────────────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+$GLOBALS['pr_test_postmeta']      = [];
+$GLOBALS['pr_test_is_singular']   = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$GLOBALS['pr_test_the_id']        = 0;
+
+// Stub the peptide repository — returned when find_by_id is called.
+$GLOBALS['pr_test_peptide_dto']   = null;
+
+if ( ! function_exists( 'get_post_meta' ) ) {
+	function get_post_meta( $post_id, string $key, bool $single = false ) {
+		if ( $single ) {
+			return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+		}
+		return array_values( $GLOBALS['pr_test_postmeta'][ (int) $post_id ] ?? [] );
+	}
+}
+
+if ( ! function_exists( 'get_permalink' ) ) {
+	function get_permalink( $post_id = null ): string {
+		return 'https://peptiderepo.com/peptides/bpc-157/';
+	}
+}
+
+if ( ! function_exists( 'get_the_ID' ) ) {
+	function get_the_ID(): int {
+		return $GLOBALS['pr_test_the_id'];
+	}
+}
+
+if ( ! function_exists( 'is_singular' ) ) {
+	function is_singular( $type = '' ): bool {
+		if ( '' === $type ) {
+			return $GLOBALS['pr_test_is_singular'];
+		}
+		return $GLOBALS['pr_test_is_singular'] && ( $GLOBALS['pr_test_singular_type'] === $type );
+	}
+}
+
+if ( ! function_exists( 'get_post_modified_time' ) ) {
+	function get_post_modified_time( $format, $gmt, $post_id ) {
+		return '2026-06-13';
+	}
+}
+
+if ( ! function_exists( 'get_userdata' ) ) {
+	function get_userdata( int $id ) {
+		return false;
+	}
+}
+
+if ( ! function_exists( 'get_author_posts_url' ) ) {
+	function get_author_posts_url( int $id ): string {
+		return 'https://peptiderepo.com/author/' . $id;
+	}
+}
+
+if ( ! function_exists( 'home_url' ) ) {
+	function home_url( string $path = '' ): string {
+		return 'https://peptiderepo.com' . $path;
+	}
+}
+
+if ( ! function_exists( 'apply_filters' ) ) {
+	function apply_filters( string $tag, $value ) {
+		return $value;
+	}
+}
+
+if ( ! function_exists( 'esc_html' ) ) {
+	function esc_html( string $val ): string {
+		return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
+	}
+}
+
+if ( ! function_exists( 'esc_html__' ) ) {
+	function esc_html__( string $text, string $domain = '' ): string {
+		return $text;
+	}
+}
+
+if ( ! function_exists( 'wp_strip_all_tags' ) ) {
+	function wp_strip_all_tags( $value ): string {
+		return strip_tags( (string) $value );
+	}
+}
+
+if ( ! function_exists( 'sanitize_textarea_field' ) ) {
+	function sanitize_textarea_field( $value ): string {
+		return is_scalar( $value ) ? trim( (string) $value ) : '';
+	}
+}
+
+// ── Stub PR_Core_Peptide_Repository ──────────────────────────────────────
+
+/**
+ * Minimal repository stub — returns whatever is in $GLOBALS['pr_test_peptide_dto'].
+ */
+class PR_Core_Peptide_Repository {
+	public function find_by_id( int $id ): ?PR_Core_Peptide_DTO {
+		return $GLOBALS['pr_test_peptide_dto'];
+	}
+}
+
+// ── Load classes under test ───────────────────────────────────────────────
+
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/dto/class-pr-core-peptide-dto.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-drug.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
+
+// ── Helper ────────────────────────────────────────────────────────────────
+
+/**
+ * Create a minimal PR_Core_Peptide_DTO for testing.
+ *
+ * @param array<string, mixed> $overrides Field overrides.
+ * @return PR_Core_Peptide_DTO
+ */
+function make_peptide_piece_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
+	return new PR_Core_Peptide_DTO( array_merge( [
+		'id'                      => 36,
+		'title'                   => 'BPC-157',
+		'slug'                    => 'bpc-157',
+		'content'                 => '',
+		'excerpt'                 => 'A synthetic pentadecapeptide.',
+		'status'                  => 'publish',
+		'display_name'            => 'BPC-157',
+		'aliases'                 => [],
+		'molecular_formula'       => '',
+		'molecular_weight'        => 0.0,
+		'cas_number'              => '',
+		'drugbank_id'             => '',
+		'chembl_id'               => '',
+		'evidence_strength'       => 'preclinical',
+		'editorial_review_status' => 'published',
+		'last_editorial_review_at' => '',
+		'medical_editor_id'       => 0,
+		'categories'              => [],
+		'families'                => [],
+	], $overrides ) );
+}
+
+echo "== JSON-LD peptide-piece regression tests (v0.6.2) ==\n\n";
+
+// ── Setup ─────────────────────────────────────────────────────────────────
+
+$GLOBALS['pr_test_the_id']        = 36;
+$GLOBALS['pr_test_is_singular']   = true;
+$GLOBALS['pr_test_singular_type'] = PR_Core_Peptide_CPT::POST_TYPE;
+$GLOBALS['pr_test_postmeta'][36]  = [
+	'_pr_molecular_formula' => 'C62H98N16O22',
+	'_pr_molecular_weight'  => '1419.5',
+	'_pr_aliases'           => '["Body Protection Compound"]',
+];
+$GLOBALS['pr_test_peptide_dto']   = make_peptide_piece_dto();
+
+$jsonld = new PR_Core_Jsonld();
+
+// ── Regression: inject_graph_pieces fatal reproduced against old contract ─
+
+echo "Regression: inject_graph_pieces (OLD hook) with plain array fatal:\n";
+
+// Simulate what Yoast's filter_graph_pieces_to_generate does:
+// it calls get_class($piece) on every item. A plain array causes a fatal.
+$drug_builder = new PR_Core_Jsonld_Drug();
+$drug_array   = $drug_builder->build( $GLOBALS['pr_test_peptide_dto'] );
+
+$caught_fatal = false;
+try {
+	// This is the exact operation Yoast does in filter_graph_pieces_to_generate().
+	// Against the old v0.6.1 code (inject via wpseo_schema_graph_pieces), this would
+	// produce: "get_class(): Argument #1 ($object) must be of type object, array given"
+	$class_result = get_class( $drug_array );
+} catch ( TypeError $e ) {
+	$caught_fatal = true;
+} catch ( Error $e ) {
+	$caught_fatal = true;
+}
+pr_assert( $caught_fatal, 'get_class(array) throws TypeError/Error — confirms the v0.6.1 fatal' );
+
+// ── Fix: inject_graph_nodes (NEW hook) works without fatal ────────────────
+
+echo "\nFix: inject_graph_nodes via wpseo_schema_graph (plain array graph):\n";
+
+// The new inject_graph_nodes method receives an already-built graph (array of arrays).
+// We simulate the wpseo_schema_graph filter call: $graph = array of plain arrays.
+$existing_graph = [
+	[
+		'@type' => 'MedicalWebPage',
+		'@id'   => 'https://peptiderepo.com/peptides/bpc-157/#webpage',
+		'name'  => 'BPC-157',
+	],
+	[
+		'@type' => 'BreadcrumbList',
+		'@id'   => 'https://peptiderepo.com/peptides/bpc-157/#breadcrumb',
+	],
+];
+
+// This must NOT throw and must append Drug node.
+$threw = false;
+try {
+	$result_graph = $jsonld->inject_graph_nodes( $existing_graph, null );
+} catch ( Throwable $e ) {
+	$threw = true;
+}
+
+pr_assert( ! $threw, 'inject_graph_nodes does NOT throw (no get_class/is_needed calls)' );
+pr_assert( count( $result_graph ) > count( $existing_graph ), 'inject_graph_nodes appended at least one node' );
+
+// Drug node must be present.
+$drug_nodes = array_filter(
+	$result_graph,
+	static function ( $node ) {
+		$types = is_array( $node['@type'] ?? null ) ? $node['@type'] : [ $node['@type'] ?? '' ];
+		return in_array( 'Drug', $types, true );
+	}
+);
+pr_assert( count( $drug_nodes ) === 1, 'exactly one Drug node in graph after inject' );
+
+$drug_node = array_values( $drug_nodes )[0];
+pr_assert_equals(
+	'https://peptiderepo.com/peptides/bpc-157/#drug',
+	$drug_node['@id'],
+	'Drug @id = {permalink}#drug'
+);
+pr_assert( isset( $drug_node['molecularFormula'] ), 'Drug has molecularFormula' );
+pr_assert( isset( $drug_node['molecularWeight'] ), 'Drug has molecularWeight (QuantitativeValue)' );
+pr_assert_equals( 'QuantitativeValue', $drug_node['molecularWeight']['@type'], 'molecularWeight @type is QuantitativeValue' );
+pr_assert_equals( 1419.5, $drug_node['molecularWeight']['value'], 'molecularWeight value correct' );
+pr_assert_equals( 'g/mol', $drug_node['molecularWeight']['unitText'], 'molecularWeight unitText = g/mol' );
+pr_assert( isset( $drug_node['alternateName'] ), 'Drug has alternateName' );
+
+// Original WebPage + BreadcrumbList nodes must be preserved.
+$webpage_nodes = array_filter( $result_graph, static fn( $n ) => ( $n['@type'] ?? '' ) === 'MedicalWebPage' );
+pr_assert( count( $webpage_nodes ) === 1, 'MedicalWebPage node preserved (no duplicate)' );
+
+$breadcrumb_nodes = array_filter( $result_graph, static fn( $n ) => ( $n['@type'] ?? '' ) === 'BreadcrumbList' );
+pr_assert( count( $breadcrumb_nodes ) === 1, 'BreadcrumbList node preserved (no duplicate)' );
+
+// ── FAQ: present when _pr_faq_items has items ─────────────────────────────
+
+echo "\nFAQ injection via inject_graph_nodes:\n";
+
+$GLOBALS['pr_test_postmeta'][36]['_pr_faq_items'] = wp_json_encode( [
+	[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic pentadecapeptide.' ],
+	[ 'question' => 'Is it safe?', 'answer' => 'Research use only; not approved for human therapy.' ],
+] );
+
+$result_with_faq = $jsonld->inject_graph_nodes( $existing_graph, null );
+
+$faq_nodes = array_filter(
+	$result_with_faq,
+	static fn( $n ) => ( $n['@type'] ?? '' ) === 'FAQPage'
+);
+pr_assert( count( $faq_nodes ) === 1, 'FAQPage node injected when _pr_faq_items has items' );
+
+$faq_node = array_values( $faq_nodes )[0];
+pr_assert_equals( 'https://peptiderepo.com/peptides/bpc-157/#faq', $faq_node['@id'], 'FAQPage @id = {permalink}#faq' );
+pr_assert( isset( $faq_node['mainEntity'] ), 'FAQPage has mainEntity' );
+pr_assert_equals( 2, count( $faq_node['mainEntity'] ), 'FAQPage has 2 questions' );
+
+// ── FAQ: absent when _pr_faq_items empty ─────────────────────────────────
+
+$GLOBALS['pr_test_postmeta'][36]['_pr_faq_items'] = '[]';
+
+$result_no_faq = $jsonld->inject_graph_nodes( $existing_graph, null );
+$faq_nodes_empty = array_filter(
+	$result_no_faq,
+	static fn( $n ) => ( $n['@type'] ?? '' ) === 'FAQPage'
+);
+pr_assert( count( $faq_nodes_empty ) === 0, 'FAQPage NOT injected when _pr_faq_items is empty array' );
+
+// ── Non-peptide page: no injection ───────────────────────────────────────
+
+echo "\nNon-peptide page: no injection:\n";
+
+$GLOBALS['pr_test_is_singular']   = false;
+$GLOBALS['pr_test_singular_type'] = '';
+
+$non_peptide_graph = [
+	[
+		'@type' => 'WebPage',
+		'@id'   => 'https://peptiderepo.com/about/#webpage',
+	],
+];
+
+$result_non_peptide = $jsonld->inject_graph_nodes( $non_peptide_graph, null );
+pr_assert( count( $result_non_peptide ) === 1, 'inject_graph_nodes no-ops on non-peptide pages (graph unchanged)' );
+
+$drug_nodes_np = array_filter( $result_non_peptide, static fn( $n ) => ( is_array( $n['@type'] ?? null ) ? in_array( 'Drug', $n['@type'], true ) : ( $n['@type'] ?? '' ) === 'Drug' ) );
+pr_assert( count( $drug_nodes_np ) === 0, 'Drug NOT injected on non-peptide page' );
+
+// ── register_hooks: does NOT hook wpseo_schema_graph_pieces ──────────────
+
+echo "\nregister_hooks: wpseo_schema_graph_pieces must NOT be hooked:\n";
+
+$GLOBALS['pr_core_test_state']['added_actions'] = [];
+$GLOBALS['pr_core_test_state']['added_filters'] = [];
+$filters_added = [];
+
+// Override add_filter in the bootstrap to capture calls.
+// (bootstrap only stubs add_action; we check via a fresh parse of register_hooks.)
+$jsonld2 = new PR_Core_Jsonld();
+
+// Use Reflection to inspect what hooks register_hooks would call.
+// Instead: inspect the class source for the string — if inject_graph_pieces is
+// still registered on wpseo_schema_graph_pieces, the bug is NOT fixed.
+$src = file_get_contents( PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php' );
+pr_assert(
+	strpos( $src, "'wpseo_schema_graph_pieces'" ) === false,
+	'class-pr-core-jsonld.php does NOT add_filter wpseo_schema_graph_pieces (correct hook removed)'
+);
+pr_assert(
+	strpos( $src, 'inject_graph_nodes' ) !== false,
+	'class-pr-core-jsonld.php references inject_graph_nodes (new method present)'
+);
+pr_assert(
+	strpos( $src, "'wpseo_schema_graph'" ) !== false,
+	'class-pr-core-jsonld.php hooks wpseo_schema_graph for injection'
+);
+
+// ── Summary ───────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

tests/unit/test-jsonld-webpage.php

@@ -0,0 +1,165 @@
+<?php
+/**
+ * Regression tests for v0.6.1: Yoast wpseo_schema_webpage_type array contract.
+ *
+ * Root cause caught on staging: v0.6.0 retype_to_medical_webpage() was
+ * strict-typed string, but Yoast passes ['WebPage'] (array) on every singular
+ * page. strict_types=1 → TypeError → HTTP 500 on all monographs + plain Pages.
+ * Secondary bug: enrich_webpage_piece compared 'WebPage' === $piece['@type']
+ * but @type is an array, so enrichment (lastReviewed/reviewedBy/audience)
+ * never injected on any page.
+ *
+ * These tests FAIL against v0.6.0 and PASS after the v0.6.1 fix.
+ *
+ * Run: php tests/unit/test-jsonld-webpage.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs ─────────────────────────────────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+$GLOBALS['pr_test_postmeta']      = [];
+$GLOBALS['pr_test_is_singular']   = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$GLOBALS['pr_test_the_id']        = 0;
+
+function get_post_meta( $post_id, string $key, bool $single = false ) {
+	if ( $single ) {
+		return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+	}
+	return array_values( $GLOBALS['pr_test_postmeta'][ (int) $post_id ] ?? [] );
+}
+
+function get_permalink( $post_id = null ): string {
+	return 'https://peptiderepo.com/peptides/bpc-157/';
+}
+
+function get_the_ID(): int {
+	return $GLOBALS['pr_test_the_id'];
+}
+
+function is_singular( $type = '' ): bool {
+	if ( '' === $type ) {
+		return $GLOBALS['pr_test_is_singular'];
+	}
+	return $GLOBALS['pr_test_is_singular'] && ( $GLOBALS['pr_test_singular_type'] === $type );
+}
+
+function get_post_modified_time( $format, $gmt, $post_id ) {
+	return '2026-04-25';
+}
+
+function get_userdata( int $id ) {
+	return false;
+}
+
+function get_author_posts_url( int $id ): string {
+	return 'https://peptiderepo.com/author/' . $id;
+}
+
+function home_url( string $path = '' ): string {
+	return 'https://peptiderepo.com' . $path;
+}
+
+function apply_filters( string $tag, $value ) {
+	return $value;
+}
+
+// Load class under test.
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
+
+echo "== JSON-LD WebPage v0.6.1 regression tests ==\n\n";
+
+$enricher = new PR_Core_Jsonld_Webpage();
+
+// ── retype_to_medical_webpage: array input, non-peptide singular ──────────
+
+echo "retype_to_medical_webpage — array input:\n";
+
+// Non-peptide singular: Yoast passes ['WebPage']; must return unchanged, no TypeError.
+$GLOBALS['pr_test_is_singular']   = true;
+$GLOBALS['pr_test_singular_type'] = 'page';  // plain WP Page, not peptide CPT.
+
+$result = $enricher->retype_to_medical_webpage( [ 'WebPage' ] );
+pr_assert_equals( [ 'WebPage' ], $result, 'non-peptide singular: array returned unchanged' );
+
+// Peptide singular: Yoast passes ['WebPage']; must return 'MedicalWebPage' (string).
+$GLOBALS['pr_test_is_singular']   = true;
+$GLOBALS['pr_test_singular_type'] = 'peptide';
+
+$result = $enricher->retype_to_medical_webpage( [ 'WebPage' ] );
+pr_assert_equals( 'MedicalWebPage', $result, 'peptide singular: returns MedicalWebPage (string)' );
+
+// String input still works (non-singular special types like CollectionPage).
+$GLOBALS['pr_test_is_singular']   = false;
+$GLOBALS['pr_test_singular_type'] = '';
+
+$result = $enricher->retype_to_medical_webpage( 'CollectionPage' );
+pr_assert_equals( 'CollectionPage', $result, 'non-singular string: passes through unchanged' );
+
+// ── enrich_webpage_piece: @type as array injects enrichments ─────────────
+
+echo "\nenrich_webpage_piece — @type as array:\n";
+
+$GLOBALS['pr_test_is_singular']   = true;
+$GLOBALS['pr_test_singular_type'] = 'peptide';
+$GLOBALS['pr_test_the_id']        = 42;
+$GLOBALS['pr_test_postmeta'][42]  = [
+	'_pr_last_reviewed' => '2026-06-01',
+];
+
+// Graph piece with @type as an array (real Yoast shape on singulars).
+$graph = [
+	[
+		'@type' => [ 'WebPage' ],
+		'@id'   => 'https://peptiderepo.com/peptides/bpc-157/#webpage',
+		'name'  => 'BPC-157',
+	],
+];
+
+$result_graph = $enricher->enrich_webpage_piece( $graph, new stdClass() );
+$piece        = $result_graph[0] ?? [];
+
+pr_assert( isset( $piece['lastReviewed'] ), '@type=array: lastReviewed injected' );
+pr_assert_equals( '2026-06-01', $piece['lastReviewed'], '@type=array: lastReviewed value correct' );
+pr_assert( isset( $piece['reviewedBy'] ), '@type=array: reviewedBy injected' );
+pr_assert( isset( $piece['audience'] ), '@type=array: audience injected' );
+
+// Also works when @type is 'MedicalWebPage' (string — after our retype fires first).
+$graph_retyed = [
+	[
+		'@type' => 'MedicalWebPage',
+		'@id'   => 'https://peptiderepo.com/peptides/bpc-157/#webpage',
+		'name'  => 'BPC-157',
+	],
+];
+
+$result_retyped = $enricher->enrich_webpage_piece( $graph_retyed, new stdClass() );
+pr_assert( isset( $result_retyped[0]['lastReviewed'] ), 'MedicalWebPage string @type: enrichment injects' );
+
+// Non-peptide page: enrichment must NOT fire even with array @type.
+$GLOBALS['pr_test_is_singular']   = true;
+$GLOBALS['pr_test_singular_type'] = 'page';
+
+$graph_non_peptide = [
+	[
+		'@type' => [ 'WebPage' ],
+		'@id'   => 'https://peptiderepo.com/about/#webpage',
+	],
+];
+
+$result_non_peptide = $enricher->enrich_webpage_piece( $graph_non_peptide, new stdClass() );
+pr_assert( ! isset( $result_non_peptide[0]['lastReviewed'] ), 'non-peptide: lastReviewed NOT injected' );
+
+// ── Summary ──────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

tests/unit/test-jsonld.php

@@ -0,0 +1,299 @@
+<?php
+/**
+ * Unit tests for v0.6.0 JSON-LD emission: Drug @id, MedicalWebPage type,
+ * FAQ conditional emission, no duplicate nodes.
+ *
+ * Run: php tests/unit/test-jsonld.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * Coverage:
+ *   - Drug node: @id = {permalink}#drug, @type includes 'Drug'.
+ *   - Drug node: molecularFormula present when _pr_molecular_formula set.
+ *   - Drug node: molecularWeight present and uses g/mol when _pr_molecular_weight set.
+ *   - Drug node: alternateName present when _pr_aliases has items.
+ *   - Drug node: molecularFormula OMITTED when meta empty.
+ *   - Drug node: molecularWeight OMITTED when meta empty.
+ *   - Drug node: alternateName OMITTED when _pr_aliases is empty array.
+ *   - FAQPage: present when _pr_faq_items has items.
+ *   - FAQPage: absent when _pr_faq_items is empty or '[]'.
+ *   - FAQPage: @id = {permalink}#faq.
+ *   - MedicalWebPage retype: retype_to_medical_webpage() returns 'MedicalWebPage' on peptide singles.
+ *   - MedicalWebPage retype: passes through unchanged on non-peptide pages.
+ *   - No duplicate WebPage or BreadcrumbList nodes emitted by our code.
+ *   - PR_Core_Schema_Sanitizers::sanitize_faq_items() validation.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs ─────────────────────────────────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+$GLOBALS['pr_test_postmeta']     = [];
+$GLOBALS['pr_test_is_singular']  = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$GLOBALS['pr_test_the_id']       = 0;
+
+function get_post_meta( $post_id, string $key, bool $single = false ) {
+	if ( $single ) {
+		return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+	}
+	return array_values( $GLOBALS['pr_test_postmeta'][ (int) $post_id ] ?? [] );
+}
+
+function get_permalink( $post_id = null ): string {
+	return 'https://peptiderepo.com/peptides/bpc-157/';
+}
+
+function get_the_ID(): int {
+	return $GLOBALS['pr_test_the_id'];
+}
+
+function is_singular( $type = '' ): bool {
+	if ( '' === $type ) {
+		return $GLOBALS['pr_test_is_singular'];
+	}
+	return $GLOBALS['pr_test_is_singular'] && ( $GLOBALS['pr_test_singular_type'] === $type );
+}
+
+function get_post_modified_time( $format, $gmt, $post_id ) {
+	return '2026-04-25';
+}
+
+function get_post_meta_val( $post_id, $key ) {
+	return $GLOBALS['pr_test_postmeta'][ (int) $post_id ][ $key ] ?? '';
+}
+
+function get_userdata( int $id ) {
+	return false;
+}
+
+function get_author_posts_url( int $id ): string {
+	return 'https://peptiderepo.com/author/' . $id;
+}
+
+function home_url( string $path = '' ): string {
+	return 'https://peptiderepo.com' . $path;
+}
+
+function apply_filters( string $tag, $value ) {
+	return $value; // No-op in test context.
+}
+
+function esc_html( string $val ): string {
+	return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
+}
+
+function esc_html__( string $text, string $domain = '' ): string {
+	return $text;
+}
+
+function wp_strip_all_tags( $value ): string {
+	return strip_tags( (string) $value );
+}
+
+function sanitize_textarea_field( $value ): string {
+	return is_scalar( $value ) ? trim( (string) $value ) : '';
+}
+
+// Load classes under test.
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/dto/class-pr-core-peptide-dto.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-drug.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-faq.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld-webpage.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/frontend/class-pr-core-jsonld.php';
+
+// ── Helpers ──────────────────────────────────────────────────────────────
+
+/**
+ * Create a minimal PR_Core_Peptide_DTO for testing.
+ *
+ * @param array<string, mixed> $overrides Field overrides.
+ * @return PR_Core_Peptide_DTO
+ */
+function make_peptide_dto( array $overrides = [] ): PR_Core_Peptide_DTO {
+	return new PR_Core_Peptide_DTO( array_merge( [
+		'id'                => 1,
+		'title'             => 'BPC-157',
+		'slug'              => 'bpc-157',
+		'content'           => '',
+		'excerpt'           => 'A synthetic peptide.',
+		'status'            => 'publish',
+		'display_name'      => 'BPC-157',
+		'aliases'           => [],
+		'molecular_formula' => '',
+		'molecular_weight'  => 0.0,
+		'cas_number'        => '',
+		'drugbank_id'       => '',
+		'chembl_id'         => '',
+		'evidence_strength' => 'preclinical',
+		'editorial_review_status' => 'published',
+		'last_editorial_review_at' => '',
+		'medical_editor_id' => 0,
+		'categories'        => [],
+		'families'          => [],
+	], $overrides ) );
+}
+
+echo "== JSON-LD v0.6.0 unit tests ==\n\n";
+
+// ── Drug @id ─────────────────────────────────────────────────────────────
+
+echo "Drug @id:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$peptide   = make_peptide_dto();
+$drug_node = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( isset( $drug_node['@id'] ), 'Drug node has @id' );
+pr_assert_equals(
+	'https://peptiderepo.com/peptides/bpc-157/#drug',
+	$drug_node['@id'],
+	'Drug @id = {permalink}#drug'
+);
+
+// ── Drug @type ───────────────────────────────────────────────────────────
+
+echo "\nDrug @type:\n";
+pr_assert( is_array( $drug_node['@type'] ), 'Drug @type is an array' );
+pr_assert( in_array( 'Drug', $drug_node['@type'], true ), '@type includes "Drug"' );
+pr_assert( in_array( 'MolecularEntity', $drug_node['@type'], true ), '@type includes "MolecularEntity"' );
+
+// ── Fields present when meta set ─────────────────────────────────────────
+
+echo "\nFields present when _pr_* meta set:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_molecular_formula' => 'C62H98N16O22',
+	'_pr_molecular_weight'  => '1419.5',
+	'_pr_aliases'           => '["Body Protection Compound-157","PL 14736"]',
+];
+
+$drug_node_populated = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( isset( $drug_node_populated['molecularFormula'] ), 'molecularFormula present when meta set' );
+pr_assert_equals( 'C62H98N16O22', $drug_node_populated['molecularFormula'], 'molecularFormula value correct' );
+
+pr_assert( isset( $drug_node_populated['molecularWeight'] ), 'molecularWeight present when meta set' );
+pr_assert_equals( 'QuantitativeValue', $drug_node_populated['molecularWeight']['@type'], 'molecularWeight @type is QuantitativeValue' );
+pr_assert_equals( 1419.5, $drug_node_populated['molecularWeight']['value'], 'molecularWeight value correct' );
+pr_assert_equals( 'g/mol', $drug_node_populated['molecularWeight']['unitText'], 'molecularWeight unitText = g/mol' );
+
+pr_assert( isset( $drug_node_populated['alternateName'] ), 'alternateName present when _pr_aliases set' );
+pr_assert_equals( 2, count( $drug_node_populated['alternateName'] ), 'alternateName has correct count' );
+
+// ── Fields omitted when meta empty ───────────────────────────────────────
+
+echo "\nFields OMITTED when meta empty:\n";
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$drug_node_empty = ( new PR_Core_Jsonld_Drug() )->build( $peptide );
+
+pr_assert( ! isset( $drug_node_empty['molecularFormula'] ), 'molecularFormula OMITTED when meta empty' );
+pr_assert( ! isset( $drug_node_empty['molecularWeight'] ), 'molecularWeight OMITTED when meta empty' );
+pr_assert( ! isset( $drug_node_empty['alternateName'] ), 'alternateName OMITTED when _pr_aliases empty' );
+
+// ── FAQPage present when _pr_faq_items has items ─────────────────────────
+
+echo "\nFAQPage emission:\n";
+
+$faq_builder = new PR_Core_Jsonld_Faq();
+$permalink   = 'https://peptiderepo.com/peptides/bpc-157/';
+
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_faq_items' => wp_json_encode( [
+		[ 'question' => 'What is BPC-157?', 'answer' => 'A synthetic peptide.' ],
+		[ 'question' => 'Is it legal?', 'answer' => 'Research use only.' ],
+	] ),
+];
+
+$faq_piece = $faq_builder->build( 1, $permalink );
+pr_assert( null !== $faq_piece, 'FAQPage piece not null when items present' );
+pr_assert_equals( 'FAQPage', $faq_piece['@type'], 'FAQPage @type correct' );
+pr_assert_equals( $permalink . '#faq', $faq_piece['@id'], 'FAQPage @id = {permalink}#faq' );
+pr_assert( isset( $faq_piece['mainEntity'] ), 'FAQPage has mainEntity' );
+pr_assert_equals( 2, count( $faq_piece['mainEntity'] ), 'FAQPage has 2 questions' );
+pr_assert_equals( 'Question', $faq_piece['mainEntity'][0]['@type'], 'Question @type correct' );
+pr_assert( isset( $faq_piece['mainEntity'][0]['acceptedAnswer'] ), 'Question has acceptedAnswer' );
+
+// ── FAQPage absent when _pr_faq_items empty ──────────────────────────────
+
+$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => '[]' ];
+$faq_empty = $faq_builder->build( 1, $permalink );
+pr_assert( null === $faq_empty, 'FAQPage piece IS null when _pr_faq_items is "[]"' );
+
+$GLOBALS['pr_test_postmeta'][1] = [];
+$faq_absent = $faq_builder->build( 1, $permalink );
+pr_assert( null === $faq_absent, 'FAQPage piece IS null when _pr_faq_items absent' );
+
+// ── MedicalWebPage retype ────────────────────────────────────────────────
+
+echo "\nMedicalWebPage retype:\n";
+
+$webpage_enricher = new PR_Core_Jsonld_Webpage();
+
+$GLOBALS['pr_test_is_singular']  = true;
+$GLOBALS['pr_test_singular_type'] = 'peptide';
+$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
+pr_assert_equals( 'MedicalWebPage', $result, 'returns MedicalWebPage on peptide single' );
+
+$GLOBALS['pr_test_is_singular']  = false;
+$GLOBALS['pr_test_singular_type'] = '';
+$result = $webpage_enricher->retype_to_medical_webpage( 'WebPage' );
+pr_assert_equals( 'WebPage', $result, 'passes through unchanged on non-peptide pages' );
+
+// ── No duplicate WebPage / BreadcrumbList nodes ───────────────────────────
+
+echo "\nNo duplicate WebPage/BreadcrumbList nodes:\n";
+
+// Verify our builders only produce Drug and FAQPage — never WebPage or BreadcrumbList.
+$GLOBALS['pr_test_postmeta'][1] = [ '_pr_faq_items' => wp_json_encode( [ [ 'question' => 'Q', 'answer' => 'A' ] ] ) ];
+$types_from_builders = [];
+foreach ( [ $drug_node_populated, $faq_piece ] as $piece ) {
+	if ( null === $piece ) { continue; }
+	$t = $piece['@type'] ?? '';
+	foreach ( ( is_array( $t ) ? $t : [ $t ] ) as $type ) {
+		$types_from_builders[] = $type;
+	}
+}
+pr_assert( ! in_array( 'WebPage', $types_from_builders, true ), 'WebPage NOT in our emitted pieces' );
+pr_assert( ! in_array( 'MedicalWebPage', $types_from_builders, true ), 'MedicalWebPage NOT in injected pieces (Yoast owns node)' );
+pr_assert( ! in_array( 'BreadcrumbList', $types_from_builders, true ), 'BreadcrumbList NOT in our emitted pieces' );
+pr_assert( in_array( 'Drug', $types_from_builders, true ), 'Drug IS in our emitted pieces' );
+pr_assert( in_array( 'FAQPage', $types_from_builders, true ), 'FAQPage IS in our emitted pieces when items present' );
+
+// ── PR_Core_Schema_Sanitizers::sanitize_faq_items() ──────────────────────
+
+echo "\nPR_Core_Schema_Sanitizers::sanitize_faq_items():\n";
+
+$valid_input = wp_json_encode( [
+	[ 'question' => 'What is BPC-157?', 'answer' => 'A peptide.' ],
+] );
+$result = PR_Core_Schema_Sanitizers::sanitize_faq_items( $valid_input );
+$decoded = json_decode( $result, true );
+pr_assert( is_array( $decoded ), 'sanitize_faq_items returns JSON-decodable string' );
+pr_assert_equals( 1, count( $decoded ), 'correct count after sanitize' );
+
+$result_empty = PR_Core_Schema_Sanitizers::sanitize_faq_items( '[]' );
+pr_assert_equals( '[]', $result_empty, 'empty JSON array returns "[]"' );
+
+$result_malformed = PR_Core_Schema_Sanitizers::sanitize_faq_items( 'not-json' );
+pr_assert_equals( '[]', $result_malformed, 'malformed JSON returns "[]"' );
+
+// Item missing 'answer' key: should be dropped.
+$incomplete_input = wp_json_encode( [ [ 'question' => 'No answer here?' ] ] );
+$result_incomplete = PR_Core_Schema_Sanitizers::sanitize_faq_items( $incomplete_input );
+$decoded_incomplete = json_decode( $result_incomplete, true );
+pr_assert_equals( 0, count( $decoded_incomplete ), 'item without answer field dropped' );
+
+// ── Summary ──────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

tests/unit/test-migration-0004.php

@@ -0,0 +1,322 @@
+<?php
+/**
+ * Unit tests for PR_Core_Migration_0004_Backfill_Peptide_Meta.
+ *
+ * Run: php tests/unit/test-migration-0004.php
+ * Exit 0 = all pass, 1 = any failure.
+ *
+ * Coverage:
+ *   - parse_weight(): strips "Da" suffix, strips "DA" variant, handles plain float,
+ *     handles empty string (returns 0.0), handles zero-value string.
+ *   - parse_aliases_string(): splits comma-separated string, trims whitespace,
+ *     drops empty segments, returns '[]' for empty input.
+ *   - PR_Core_Schema_Sanitizers::sanitize_molecular_formula(): valid chars, strips HTML, strips invalid.
+ *   - Idempotency: backfill_post() returns 'skipped' when all three PR Core keys populated.
+ *   - PSA source path: copies and transforms psa_* values to _pr_* keys.
+ *   - Empty PSA data: skips to pubchem path, returns 'pubchem_skip' on no data.
+ *
+ * Not covered here (require live WP + DB or network):
+ *   - PubChem HTTP round-trip (mocked at the http_get_once level in integration tests).
+ *   - Actual update_post_meta() persistence.
+ *
+ * @package PeptideRepoCore
+ */
+
+declare(strict_types=1);
+
+// Bootstrap the lightweight WP stubs.
+require_once __DIR__ . '/../bootstrap.php';
+
+// ── Additional stubs needed for migration 0004 ──────────────────────────
+
+if ( ! defined( 'PR_CORE_TARGET_SCHEMA_VERSION' ) ) {
+	define( 'PR_CORE_TARGET_SCHEMA_VERSION', 4 );
+}
+
+// Post meta store for testing.
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+
+function get_post_meta( int $post_id, string $key, bool $single = false ) {
+	$store = $GLOBALS['pr_test_postmeta'][ $post_id ] ?? [];
+	return $single ? ( $store[ $key ] ?? '' ) : array_values( $store );
+}
+
+function update_post_meta( int $post_id, string $key, $value ): bool {
+	$GLOBALS['pr_test_postmeta'][ $post_id ][ $key ] = $value;
+	$GLOBALS['pr_test_updated_meta'][]                = [ 'post_id' => $post_id, 'key' => $key, 'value' => $value ];
+	return true;
+}
+
+function get_post( int $id ) {
+	if ( isset( $GLOBALS['pr_test_posts'][ $id ] ) ) {
+		return $GLOBALS['pr_test_posts'][ $id ];
+	}
+	return null;
+}
+
+function get_posts( array $args = [] ): array {
+	return $GLOBALS['pr_test_all_post_ids'] ?? [];
+}
+
+function is_wp_error( $value ): bool {
+	return false;
+}
+
+function wp_strip_all_tags( $value ): string {
+	return strip_tags( (string) $value );
+}
+
+function esc_html( string $val ): string {
+	return htmlspecialchars( $val, ENT_QUOTES, 'UTF-8' );
+}
+
+if ( ! function_exists( 'error_log' ) ) {
+	function error_log( string $msg ): bool {
+		// Suppress during tests.
+		return true;
+	}
+}
+
+// Load dependencies.
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-schema-sanitizers.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/cpt/class-pr-core-peptide-cpt.php';
+require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-pubchem-client.php';
+// Load migration class under test.
+require_once PR_CORE_PLUGIN_DIR . 'includes/migrations/class-pr-core-migration-0004-backfill-peptide-meta.php';
+
+// ── Expose private methods via reflection ────────────────────────────────
+
+/**
+ * Call a private/protected method on an object via reflection.
+ *
+ * @param object $obj        Instance.
+ * @param string $method     Method name.
+ * @param array  $args       Arguments.
+ * @return mixed Return value.
+ */
+function call_private( object $obj, string $method, array $args = [] ) {
+	$ref = new ReflectionMethod( $obj, $method );
+	$ref->setAccessible( true );
+	return $ref->invokeArgs( $obj, $args );
+}
+
+$migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta();
+
+echo "== PR_Core_Migration_0004 unit tests ==\n\n";
+
+// ── parse_weight() ───────────────────────────────────────────────────────
+
+echo "parse_weight():\n";
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5 Da' ),
+	'strips " Da" suffix and parses float'
+);
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5 DA' ),
+	'strips uppercase " DA" suffix'
+);
+
+pr_assert_equals(
+	1419.5,
+	$migration->parse_weight( '1419.5' ),
+	'parses plain float string without suffix'
+);
+
+pr_assert_equals(
+	0.0,
+	$migration->parse_weight( '' ),
+	'returns 0.0 for empty string'
+);
+
+pr_assert_equals(
+	0.0,
+	$migration->parse_weight( '  Da  ' ),
+	'returns 0.0 for suffix-only string'
+);
+
+pr_assert_equals(
+	800.123,
+	$migration->parse_weight( '  800.123 da  ' ),
+	'strips whitespace and lowercase "da"'
+);
+
+// ── parse_aliases_string() ───────────────────────────────────────────────
+
+echo "\nparse_aliases_string():\n";
+
+$result = json_decode(
+	$migration->parse_aliases_string( 'Body Protection Compound-157, PL 14736, PL-10, Bepecin' ),
+	true
+);
+pr_assert( is_array( $result ), 'returns a JSON-decodable array' );
+pr_assert_equals( 4, count( $result ), 'correct count: 4 aliases' );
+pr_assert_equals( 'Body Protection Compound-157', $result[0], 'first alias trimmed correctly' );
+pr_assert_equals( 'PL 14736', $result[1], 'second alias trimmed correctly' );
+
+$empty_result = $migration->parse_aliases_string( '' );
+pr_assert_equals( '[]', $empty_result, 'empty string returns "[]"' );
+
+$whitespace_result = $migration->parse_aliases_string( '  ,  ,  ' );
+pr_assert_equals( '[]', $whitespace_result, 'whitespace-only segments dropped, returns "[]"' );
+
+$single = json_decode( $migration->parse_aliases_string( 'Only One' ), true );
+pr_assert_equals( 1, count( $single ), 'single alias produces array of 1' );
+
+// ── sanitize_formula() ───────────────────────────────────────────────────
+// Five required cases (Option B — validate, don't allowlist):
+//   1. Valid formula unchanged.
+//   2. Parenthesised formula preserved.
+//   3. Newline-injected payload — "injection" stripped, formula kept.
+//   4. Fully invalid string (script tag contents) → empty.
+//   5. Empty / whitespace-only → empty.
+
+echo "\nPR_Core_Schema_Sanitizers::sanitize_molecular_formula():\n";
+
+pr_assert_equals(
+	'C62H98N16O22',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C62H98N16O22' ),
+	'valid formula passes unchanged'
+);
+
+pr_assert_equals(
+	'C62H98N16O22',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<b>C62H98N16O22</b>' ),
+	'HTML tags stripped from formula'
+);
+
+pr_assert_equals(
+	'C2H5(OH)',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( 'C2H5(OH)' ),
+	'parenthesised formula preserved unchanged'
+);
+
+pr_assert_equals(
+	'C10H12',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( "C10H12\ninjection" ),
+	'non-formula characters removed — newline+word stripped, formula kept'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '<script>alert(1)</script>' ),
+	'fully invalid string returns empty string'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '' ),
+	'empty string returns empty string'
+);
+
+pr_assert_equals(
+	'',
+	PR_Core_Schema_Sanitizers::sanitize_molecular_formula( '   ' ),
+	'whitespace-only returns empty string'
+);
+
+// ── Idempotency: skips when all three PR Core keys populated ─────────────
+
+echo "\nIdempotency (all _pr_* keys populated):\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][1] = [
+	'_pr_molecular_formula' => 'C62H98N16O22',
+	'_pr_molecular_weight'  => '1419.5',
+	'_pr_aliases'           => '["Alias One"]',
+];
+
+$result = call_private( $migration, 'backfill_post', [ 1 ] );
+pr_assert_equals( 'skipped', $result, 'returns "skipped" when all three keys non-empty' );
+pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no update_post_meta calls when skipped' );
+
+// ── PSA source path ──────────────────────────────────────────────────────
+
+echo "\nPSA source path:\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][2] = [
+	'psa_molecular_formula' => 'C62H98N16O22',
+	'psa_molecular_weight'  => '1419.5 Da',
+	'psa_aliases'           => 'Body Protection Compound-157, PL 14736',
+];
+$GLOBALS['pr_test_posts'][2] = (object) [ 'post_title' => 'BPC-157', 'ID' => 2 ];
+
+$result = call_private( $migration, 'backfill_post', [ 2 ] );
+pr_assert_equals( 'copied_psa', $result, 'returns "copied_psa" when PSA data present' );
+
+$updated = $GLOBALS['pr_test_updated_meta'];
+$formula_written = false;
+$weight_written  = false;
+$aliases_written = false;
+
+foreach ( $updated as $entry ) {
+	if ( '_pr_molecular_formula' === $entry['key'] ) {
+		$formula_written = true;
+		pr_assert_equals( 'C62H98N16O22', $entry['value'], 'formula written correctly' );
+	}
+	if ( '_pr_molecular_weight' === $entry['key'] ) {
+		$weight_written = true;
+		pr_assert_equals( '1419.5', $entry['value'], 'weight written as float string without Da' );
+	}
+	if ( '_pr_aliases' === $entry['key'] ) {
+		$aliases_written = true;
+		$aliases_arr     = json_decode( $entry['value'], true );
+		pr_assert( is_array( $aliases_arr ), 'aliases stored as JSON array' );
+		pr_assert_equals( 2, count( $aliases_arr ), 'correct number of aliases' );
+	}
+}
+
+pr_assert( $formula_written, 'molecular formula meta was written' );
+pr_assert( $weight_written, 'molecular weight meta was written' );
+pr_assert( $aliases_written, 'aliases meta was written' );
+
+// ── Partial re-run: existing values preserved ────────────────────────────
+
+echo "\nIdempotency: only some keys populated (partial re-run):\n";
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+// Only formula already set; weight and aliases are empty.
+$GLOBALS['pr_test_postmeta'][3] = [
+	'_pr_molecular_formula' => 'C10H12',
+	'_pr_molecular_weight'  => '',
+	'_pr_aliases'           => '',
+	'psa_molecular_formula' => 'C62H98N16O22',
+	'psa_molecular_weight'  => '1419.5 Da',
+	'psa_aliases'           => 'Body Protection Compound-157',
+];
+$GLOBALS['pr_test_posts'][3] = (object) [ 'post_title' => 'BPC-157', 'ID' => 3 ];
+
+$result = call_private( $migration, 'backfill_post', [ 3 ] );
+pr_assert_equals( 'copied_psa', $result, 'runs PSA copy even when only some keys populated' );
+
+// ── PubChem skip path: no PSA data, no network ──────────────────────────
+
+echo "\nPubChem skip path (no PSA data, no network in unit tests):\n";
+
+// Inject a null-returning PubChem client mock to simulate network failure.
+$mock_pubchem = new class extends PR_Core_Pubchem_Client {
+	public function fetch_by_cid( string $cid ): ?array { return null; }
+	public function fetch_by_name( string $name ): ?array { return null; }
+};
+$mock_migration = new PR_Core_Migration_0004_Backfill_Peptide_Meta( $mock_pubchem );
+
+$GLOBALS['pr_test_postmeta'] = [];
+$GLOBALS['pr_test_updated_meta'] = [];
+$GLOBALS['pr_test_postmeta'][10] = []; // No PSA data, no PR Core data.
+$GLOBALS['pr_test_posts'][10] = (object) [ 'post_title' => 'IGF-1 LR3', 'ID' => 10 ];
+
+$result = call_private( $mock_migration, 'backfill_post', [ 10 ] );
+pr_assert_equals( 'pubchem_skip', $result, 'returns "pubchem_skip" when PubChem network fails' );
+pr_assert( empty( $GLOBALS['pr_test_updated_meta'] ), 'no meta written on pubchem_skip' );
+
+// ── Summary ──────────────────────────────────────────────────────────────
+
+exit( pr_test_summary() );

uninstall.php

@@ -76,6 +76,31 @@ $wpdb->query(
 	"DELETE FROM {$wpdb->options} WHERE option_name LIKE 'pr\_core\_%'"
 );
 
+/* ── 4b. Delete v0.6.0 schema-input meta keys from all peptide posts ──── */
+
+/*
+ * Migration 0004 writes _pr_molecular_formula, _pr_molecular_weight, _pr_aliases,
+ * and _pr_faq_items to the shared peptide posts. These are PR Core-authored values
+ * (derived from PubChem / PSA) and are safe to remove on uninstall.
+ *
+ * @see ARCHITECTURE.md — §2.9 Uninstall specification.
+ */
+$schema_meta_keys = [
+	'_pr_molecular_formula',
+	'_pr_molecular_weight',
+	'_pr_aliases',
+	'_pr_faq_items',
+];
+
+foreach ( $schema_meta_keys as $meta_key ) {
+	// phpcs:ignore WordPress.DB.DirectDatabaseQuery.DirectQuery
+	$wpdb->delete(
+		$wpdb->postmeta,
+		[ 'meta_key' => $meta_key ],
+		[ '%s' ]
+	);
+}
+
 /* ── 5. Remove manage_peptide_content capability from all roles ───────── */
 
 $editable_roles = wp_roles()->roles;