feat: improve clinical assistant export and citations

docker-compose.yml

@@ -8,12 +8,18 @@ services:
       - .env
     environment:
       CLINICAL_ASSISTANT_MCP_URL: http://mcp:8000/mcp
+      CLINICAL_ASSISTANT_MULTIMODAL_S3_ENDPOINT: http://minio:9000
+      CLINICAL_ASSISTANT_MULTIMODAL_S3_ACCESS_KEY: ${MULTIMODAL_OBJECT_STORE_ACCESS_KEY:-minioadmin}
+      CLINICAL_ASSISTANT_MULTIMODAL_S3_SECRET_KEY: ${MULTIMODAL_OBJECT_STORE_SECRET_KEY:-minioadmin}
+      REDIS_URL: redis://ped-ai-redis:6379
     volumes:
       - scribe-logs:/app/data/logs
       - clinical-assistant-mcp-data:/app/mcp-data:ro
     depends_on:
       postgres:
         condition: service_healthy
+      redis:
+        condition: service_healthy
     restart: unless-stopped
     container_name: pediatric-ai-scribe
     networks:
@@ -46,9 +52,26 @@ services:
       retries: 5
       start_period: 10s
 
+  redis:
+    image: redis:8-alpine
+    command: redis-server --appendonly yes
+    restart: unless-stopped
+    container_name: ped-ai-redis
+    volumes:
+      - redis-data:/data
+    healthcheck:
+      test: ["CMD", "redis-cli", "ping"]
+      interval: 10s
+      timeout: 5s
+      retries: 5
+    networks:
+      - default
+      - mcp-server_default
+
 volumes:
   pgdata:
   scribe-logs:
+  redis-data:
   clinical-assistant-mcp-data:
     external: true
     name: mcp-server_mcp-data

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "pediatric-ai-scribe",
-  "version": "7.0.0",
+  "version": "7.7.0",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "pediatric-ai-scribe",
-      "version": "7.0.0",
+      "version": "7.7.0",
       "dependencies": {
         "@marp-team/marp-cli": "^4.3.1",
         "@marp-team/marp-core": "^4.3.0",
@@ -28,6 +28,7 @@
         "helmet": "^8.0.0",
         "jsonwebtoken": "^9.0.2",
         "mammoth": "^1.8.0",
+        "markdown-it": "^14.1.1",
         "marked": "^18.0.2",
         "multer": "^1.4.5-lts.1",
         "node-pg-migrate": "^7.7.0",
@@ -38,6 +39,7 @@
         "pg": "^8.13.0",
         "pptxgenjs": "^4.0.1",
         "qrcode": "^1.5.4",
+        "redis": "^4.7.1",
         "speakeasy": "^2.0.0"
       },
       "devDependencies": {
@@ -2471,6 +2473,65 @@
         "node": ">=12"
       }
     },
+    "node_modules/@redis/bloom": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/@redis/bloom/-/bloom-1.2.0.tgz",
+      "integrity": "sha512-HG2DFjYKbpNmVXsa0keLHp/3leGJz1mjh09f2RLGGLQZzSHpkmZWuwJbAvo3QcRY8p80m5+ZdXZdYOSBLlp7Cg==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@redis/client": "^1.0.0"
+      }
+    },
+    "node_modules/@redis/client": {
+      "version": "1.6.1",
+      "resolved": "https://registry.npmjs.org/@redis/client/-/client-1.6.1.tgz",
+      "integrity": "sha512-/KCsg3xSlR+nCK8/8ZYSknYxvXHwubJrU82F3Lm1Fp6789VQ0/3RJKfsmRXjqfaTA++23CvC3hqmqe/2GEt6Kw==",
+      "license": "MIT",
+      "dependencies": {
+        "cluster-key-slot": "1.1.2",
+        "generic-pool": "3.9.0",
+        "yallist": "4.0.0"
+      },
+      "engines": {
+        "node": ">=14"
+      }
+    },
+    "node_modules/@redis/graph": {
+      "version": "1.1.1",
+      "resolved": "https://registry.npmjs.org/@redis/graph/-/graph-1.1.1.tgz",
+      "integrity": "sha512-FEMTcTHZozZciLRl6GiiIB4zGm5z5F3F6a6FZCyrfxdKOhFlGkiAqlexWMBzCi4DcRoyiOsuLfW+cjlGWyExOw==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@redis/client": "^1.0.0"
+      }
+    },
+    "node_modules/@redis/json": {
+      "version": "1.0.7",
+      "resolved": "https://registry.npmjs.org/@redis/json/-/json-1.0.7.tgz",
+      "integrity": "sha512-6UyXfjVaTBTJtKNG4/9Z8PSpKE6XgSyEb8iwaqDcy+uKrd/DGYHTWkUdnQDyzm727V7p21WUMhsqz5oy65kPcQ==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@redis/client": "^1.0.0"
+      }
+    },
+    "node_modules/@redis/search": {
+      "version": "1.2.0",
+      "resolved": "https://registry.npmjs.org/@redis/search/-/search-1.2.0.tgz",
+      "integrity": "sha512-tYoDBbtqOVigEDMAcTGsRlMycIIjwMCgD8eR2t0NANeQmgK/lvxNAvYyb6bZDD4frHRhIHkJu2TBRvB0ERkOmw==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@redis/client": "^1.0.0"
+      }
+    },
+    "node_modules/@redis/time-series": {
+      "version": "1.1.0",
+      "resolved": "https://registry.npmjs.org/@redis/time-series/-/time-series-1.1.0.tgz",
+      "integrity": "sha512-c1Q99M5ljsIuc4YdaCwfUEXsofakb9c8+Zse2qxTadu8TalLXuAESzLvFAvNVbkmSlvlzIQOLpBCmWI9wTOt+g==",
+      "license": "MIT",
+      "peerDependencies": {
+        "@redis/client": "^1.0.0"
+      }
+    },
     "node_modules/@remirror/core-constants": {
       "version": "3.0.0",
       "resolved": "https://registry.npmjs.org/@remirror/core-constants/-/core-constants-3.0.0.tgz",
@@ -4276,6 +4337,15 @@
         "wrap-ansi": "^6.2.0"
       }
     },
+    "node_modules/cluster-key-slot": {
+      "version": "1.1.2",
+      "resolved": "https://registry.npmjs.org/cluster-key-slot/-/cluster-key-slot-1.1.2.tgz",
+      "integrity": "sha512-RMr0FhtfXemyinomL4hrWcYJxmX6deFdCxpJzhDttxgO1+bcCnkk+9drydLVDmAMG7NE6aN/fl4F7ucU/90gAA==",
+      "license": "Apache-2.0",
+      "engines": {
+        "node": ">=0.10.0"
+      }
+    },
     "node_modules/color-convert": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/color-convert/-/color-convert-2.0.1.tgz",
@@ -5322,6 +5392,15 @@
         "node": ">=14"
       }
     },
+    "node_modules/generic-pool": {
+      "version": "3.9.0",
+      "resolved": "https://registry.npmjs.org/generic-pool/-/generic-pool-3.9.0.tgz",
+      "integrity": "sha512-hymDOu5B53XvN4QT9dBmZxPX4CWhBPPLguTZ9MMFeFa/Kg0xWVfylOVNlJji/E7yTZWFd/q9GO5TxDLq156D7g==",
+      "license": "MIT",
+      "engines": {
+        "node": ">= 4"
+      }
+    },
     "node_modules/get-caller-file": {
       "version": "2.0.5",
       "resolved": "https://registry.npmjs.org/get-caller-file/-/get-caller-file-2.0.5.tgz",
@@ -7746,6 +7825,23 @@
         "url": "https://paulmillr.com/funding/"
       }
     },
+    "node_modules/redis": {
+      "version": "4.7.1",
+      "resolved": "https://registry.npmjs.org/redis/-/redis-4.7.1.tgz",
+      "integrity": "sha512-S1bJDnqLftzHXHP8JsT5II/CtHWQrASX5K96REjWjlmWKrviSOLWmM7QnRLstAWsu1VBBV1ffV6DzCvxNP0UJQ==",
+      "license": "MIT",
+      "workspaces": [
+        "./packages/*"
+      ],
+      "dependencies": {
+        "@redis/bloom": "1.2.0",
+        "@redis/client": "1.6.1",
+        "@redis/graph": "1.1.1",
+        "@redis/json": "1.0.7",
+        "@redis/search": "1.2.0",
+        "@redis/time-series": "1.1.0"
+      }
+    },
     "node_modules/require-directory": {
       "version": "2.1.1",
       "resolved": "https://registry.npmjs.org/require-directory/-/require-directory-2.1.1.tgz",
@@ -8745,6 +8841,12 @@
       "integrity": "sha512-JKhqTOwSrqNA1NY5lSztJ1GrBiUodLMmIZuLiDaMRJ+itFd+ABVE8XBjOvIWL+rSqNDC74LCSFmlb/U4UZ4hJQ==",
       "license": "ISC"
     },
+    "node_modules/yallist": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
+      "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==",
+      "license": "ISC"
+    },
     "node_modules/yargs": {
       "version": "15.4.1",
       "resolved": "https://registry.npmjs.org/yargs/-/yargs-15.4.1.tgz",

package.json

@@ -36,6 +36,7 @@
     "helmet": "^8.0.0",
     "jsonwebtoken": "^9.0.2",
     "mammoth": "^1.8.0",
+    "markdown-it": "^14.1.1",
     "marked": "^18.0.2",
     "multer": "^1.4.5-lts.1",
     "node-pg-migrate": "^7.7.0",
@@ -46,6 +47,7 @@
     "pg": "^8.13.0",
     "pptxgenjs": "^4.0.1",
     "qrcode": "^1.5.4",
+    "redis": "^4.7.1",
     "speakeasy": "^2.0.0"
   },
   "optionalDependencies": {

public/components/assistant.html

@@ -132,7 +132,8 @@
 .assistant-thinking-dot:nth-child(3) { animation-delay:.3s; margin-right:3px; }
 @keyframes assistantBounce { 0%,80%,100% { transform:scale(.65); opacity:.45; } 40% { transform:scale(1); opacity:1; } }
 @keyframes assistantShimmer { 0% { background-position:100% 0; } 100% { background-position:-100% 0; } }
-.assistant-cite { display:inline-flex; align-items:center; justify-content:center; min-width:20px; height:20px; padding:0 6px; border-radius:999px; background:var(--purple-light); color:var(--purple); font-size:11px; font-weight:700; text-decoration:none; }
+.assistant-cite { display:inline-flex; align-items:center; justify-content:center; min-width:18px; height:18px; padding:0 6px; margin:0 1px; border-radius:999px; background:var(--purple-light); color:var(--purple); font-size:10px; font-weight:800; text-decoration:none; vertical-align:baseline; border:1px solid rgba(124,58,237,.18); text-transform:uppercase; letter-spacing:.03em; }
+.assistant-cite:hover { background:var(--purple); color:white; text-decoration:none; }
 .assistant-composer { border-top:1px solid var(--g200); padding:12px; background:white; display:grid; gap:8px; }
 .assistant-composer textarea, .assistant-side textarea { width:100%; border:1.5px solid var(--g300); border-radius:10px; padding:10px 12px; resize:vertical; font-family:inherit; font-size:13px; outline:none; }
 .assistant-composer textarea:focus, .assistant-side textarea:focus { border-color:var(--blue); box-shadow:0 0 0 3px var(--blue-light); }

public/index.html

@@ -16,7 +16,7 @@
           integrity="sha384-+VfUPEb0PdtChMwmBcBmykRMDd+v6D/oFmB3rZM/puCMDYcIvF968OimRh4KQY9a"
           crossorigin="anonymous" referrerpolicy="no-referrer" defer></script>
   <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css">
-  <script src="https://cdn.jsdelivr.net/npm/marked@14.1.3/marked.min.js" defer></script>
+  <script src="/vendor/markdown-it/markdown-it.min.js" defer></script>
   <script src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" defer></script>
   <link rel="manifest" href="/manifest.json">
   <meta name="theme-color" content="#2563eb">

public/js/admin.js

@@ -665,7 +665,7 @@
 (function() {
   var loaded = false;
   var defaults = {
-    behavior: 'You are a concise pediatric clinical assistant. Use retrieved context only for factual claims. If the user input is a greeting or too vague, answer briefly and ask what they want to look up. Synthesize across sources, cite claims with numbered citations like [1], and list sources at the bottom by title/resource and page. Do not invent citations.'
+    behavior: 'You are a concise pediatric clinical assistant. Use retrieved context only for factual claims. If the user input is a greeting or too vague, answer briefly and ask what they want to look up. Synthesize across sources and cite factual claims with the exact provided source numbers like [1]. Do not invent, renumber, merge, or move citations.'
   };
 
   document.addEventListener('tabChanged', function(e) {

public/js/assistant/citations.js

@@ -1,6 +1,6 @@
 export function renderAssistantMarkdown(md, sources, options) {
   var opts = options || {};
-  var text = normalizeMarkdownText(md);
+  var text = stripOrphanMarkdownMarkers(repairTabSeparatedTables(repairMarkdownTables(normalizeMarkdownText(md))));
   var codeBlocks = [];
   text = text.replace(/```(\w+)?\n([\s\S]*?)```/g, function (_, lang, code) {
     var idx = codeBlocks.length;
@@ -12,13 +12,15 @@ export function renderAssistantMarkdown(md, sources, options) {
   text = normalizeAdjacentCitationClusters(text, sources || []);
 
   var html;
-  if (opts.marked && typeof opts.marked.parse === 'function') {
+  if (opts.markdownIt && typeof opts.markdownIt.render === 'function') {
+    html = opts.markdownIt.render(text);
+  } else if (opts.marked && typeof opts.marked.parse === 'function') {
     html = opts.marked.parse(text, { breaks: true, gfm: true });
   } else {
     html = fallbackMarkdown(text);
   }
 
-  html = renderCitationLinks(html, sources || []);
+  html = renderCitationLinks(html, sources || [], opts);
   html = html.replace(/@@CODEBLOCK_(\d+)@@/g, function (_, idx) {
     var block = codeBlocks[Number(idx)] || { lang: '', code: '' };
     if (block.lang === 'mermaid') return '<div class="assistant-mermaid" data-mermaid="' + escapeAttr(block.code) + '">Rendering graph...</div>';
@@ -29,15 +31,19 @@ export function renderAssistantMarkdown(md, sources, options) {
   return typeof opts.sanitize === 'function' ? opts.sanitize(html) : html;
 }
 
-export function renderCitationLinks(html, sources) {
+export function renderCitationLinks(html, sources, options) {
+  var opts = options || {};
   return String(html || '').replace(/\[((?:\d+\s*,\s*)*\d+)\]/g, function (match, cluster) {
     var nums = cluster.split(',').map(function (n) { return Number(n.trim()); }).filter(function (n) { return Number.isInteger(n) && n > 0; });
     if (!nums.length || nums.some(function (n) { return !sources[n - 1]; })) return match;
-    return '[' + nums.map(function (n) {
+    return nums.map(function (n) {
       var source = sources[n - 1];
       var title = source ? source.title || source.resource || 'Source' : 'Source';
-      return '<a class="assistant-cite" href="#assistant-source-' + n + '" title="' + escapeHtml(title) + '">' + n + '</a>';
+      var page = source && (source.page || source.page_number || source.pageNumber);
-    }).join(', ') + ']';
+      var label = 'Source ' + n + ': ' + title + (page ? ', page ' + page : '');
+      var text = opts.citationLabel === 'number' ? String(n) : 'src';
+      return '<a class="assistant-cite" href="#assistant-source-' + n + '" data-source-number="' + n + '" title="' + escapeHtml(label) + '" aria-label="' + escapeAttr(label) + '">' + text + '</a>';
+    }).join(' ');
   });
 }
 
@@ -85,10 +91,14 @@ export function stripSourcesSection(text) {
 }
 
 export function normalizeMarkdownText(text) {
-  return String(text || '')
+  return stripOrphanMarkdownMarkers(String(text || '')
     .replace(/\r\n/g, '\n')
-    .replace(/(\[(?:\d+\s*,\s*)*\d+\])\s*-\s+/g, '$1\n- ')
+    .replace(/(\[(?:\d+\s*,\s*)*\d+\])\s*[-–—]\s*/g, '$1\n- ')
-    .replace(/([.!?])\s*-\s+(\*\*)?/g, '$1\n- $2')
+    .replace(/([.!?])\s*[-–—]\s+(\*\*)?/g, '$1\n- $2')
+    .replace(/(:)\s*[-–—]\s+(\*\*)?/g, '$1\n- $2')
+    .replace(/(\[(?:\d+\s*,\s*)*\d+\]\.)\s+(\d+\.\s+[A-Z][A-Za-z][^\n]{0,80})/g, '$1\n$2')
+    .replace(/([.!?])\s+(\d+\.\s+[A-Z][A-Za-z][^\n]{0,80})/g, '$1\n$2')
+    .replace(/(\[(?:\d+\s*,\s*)*\d+\])(?=\s*(?:[A-Z][A-Za-z]+\s+){1,4}(?:deficits?|distress|apnoea|apnea|vomiting|seizures?|signs?|symptoms?|criteria|indications?|risk|oxygen|saturation|dehydration|lethargy|toxicity)\b)/g, '$1\n')
     .replace(/([^\n])\s+(#{1,4}\s+)/g, '$1\n\n$2')
     .replace(/(#{1,4}\s+[^\n]+?)\s+(-\s+)/g, '$1\n\n$2')
     .replace(/(#{1,4}\s+[^\n]+)\n(-\s+)/g, '$1\n\n$2')
@@ -97,7 +107,173 @@ export function normalizeMarkdownText(text) {
     .replace(/([^\n])\s+(\|\s*[-:]+\s*\|)/g, '$1\n$2')
     .replace(/\s+(\|\s*[^\n|]+\s*\|\s*[^\n|]+\s*\|)/g, '\n$1')
     .replace(/([^\n])\s+(-\s+[^\n])/g, '$1\n$2')
-    .trim();
+    .trim());
+}
+
+export function stripOrphanMarkdownMarkers(text) {
+  return String(text || '').replace(/(?:\n|^)\s*(?:\*\*|__|\*|_)\s*$/g, '').trim();
+}
+
+export function repairTabSeparatedTables(text) {
+  var lines = String(text || '').split('\n');
+  var out = [];
+  var i = 0;
+  while (i < lines.length) {
+    if (!/\t/.test(lines[i]) || i + 1 >= lines.length || !/\t/.test(lines[i + 1])) {
+      out.push(lines[i]);
+      i += 1;
+      continue;
+    }
+    if (out.length && out[out.length - 1].trim()) out.push('');
+    var tableLines = [];
+    while (i < lines.length && shouldKeepTabTableLine(lines[i], tableLines.length)) {
+      tableLines.push(lines[i]);
+      i += 1;
+    }
+    var header = tableLines[0].split('\t').map(function(cell) { return cell.trim(); });
+    var rows = tabTableRows(tableLines.slice(1), header.length);
+    out.push('| ' + header.join(' | ') + ' |');
+    out.push('| ' + header.map(function() { return '---'; }).join(' | ') + ' |');
+    rows.forEach(function(cells) {
+      out.push('| ' + cells.map(cleanTableCell).join(' | ') + ' |');
+    });
+  }
+  return out.join('\n');
+}
+
+function shouldKeepTabTableLine(line, count) {
+  if (/\t/.test(line)) return true;
+  if (!count || !String(line || '').trim()) return false;
+  if (/^\s*(#{1,6}\s+|References\b|Sources\b)/i.test(line)) return false;
+  return /^\s*(?:\d+\s*){1,4}$/.test(line) || /^[^.!?]{1,90}$/.test(line);
+}
+
+function tabTableRows(lines, width) {
+  var rows = [];
+  var pending = null;
+  lines.forEach(function(line) {
+    var cells = String(line || '').split('\t').map(function(cell) { return cell.trim(); });
+    if (cells.length === 1 && pending) {
+      pending[pending.length - 1] = [pending[pending.length - 1], cells[0]].filter(Boolean).join(' ');
+      return;
+    }
+    if (pending && cells.length >= width && looksCitationCell(cells[0]) && cells[width - 1]) {
+      pending[pending.length - 1] = [pending[pending.length - 1], cells[0]].filter(Boolean).join(' ');
+      rows.push(normalizeTabRow(pending, width));
+      pending = [cells[width - 1]];
+      return;
+    }
+    if (pending && cells.length >= width) {
+      rows.push(normalizeTabRow(pending, width));
+      pending = null;
+    }
+    if (cells.length >= width) {
+      rows.push(normalizeTabRow(cells, width));
+      return;
+    }
+    if (pending) {
+      pending[pending.length - 1] = [pending[pending.length - 1], cells.join(' ')].filter(Boolean).join(' ');
+    } else {
+      pending = cells;
+    }
+  });
+  if (pending) rows.push(normalizeTabRow(pending, width));
+  return rows;
+}
+
+function normalizeTabRow(cells, width) {
+  cells = cells.slice();
+  while (cells.length < width) cells.push('');
+  if (width === 3 && looksCitationCell(cells[0]) && cells[2]) {
+    return [cells[2], '', cells[0]];
+  }
+  if (width === 3 && /\b(\d+\s*){1,4}\s+(?:Nonoperative|Surgical|Diagnostic|Recurrence|Initial|Further)\b/i.test(cells[1] || '')) {
+    var split = splitCitationPrefix(cells[1]);
+    cells[1] = split.citation;
+    if (split.rest && cells[2]) cells[2] = split.rest + ': ' + cells[2];
+  }
+  return cells.slice(0, width);
+}
+
+function splitCitationPrefix(text) {
+  var m = String(text || '').match(/^((?:\d+\s*){1,4})\s+(.+)$/);
+  return m ? { citation: m[1].trim(), rest: m[2].trim() } : { citation: text, rest: '' };
+}
+
+function looksCitationCell(text) {
+  return /^(?:\d+\s*){1,5}$/.test(String(text || '').trim());
+}
+
+function cleanTableCell(cell) {
+  return String(cell || '').replace(/(?:^|\s+)If you need[\s\S]*$/i, '').trim();
+}
+
+export function repairMarkdownTables(text) {
+  var lines = String(text || '').split('\n');
+  var repaired = [];
+  var i = 0;
+  while (i < lines.length) {
+    if (isSplitTableHeader(lines, i)) {
+      lines[i] = mergeSplitTableRows(lines[i], lines[i + 1]);
+      lines.splice(i + 1, 1);
+    }
+    if (!isPotentialTableHeader(lines, i)) {
+      repaired.push(lines[i]);
+      i += 1;
+      continue;
+    }
+
+    var expected = tableCells(lines[i]).length;
+    if (repaired.length && repaired[repaired.length - 1].trim()) repaired.push('');
+    repaired.push(lines[i], normalizeTableSeparator(lines[i + 1], expected));
+    i += 2;
+
+    while (i < lines.length) {
+      var row = lines[i];
+      if (!row.trim()) { i += 1; continue; }
+      if (!/^\s*\|/.test(row)) break;
+
+      var merged = row;
+      var guard = 0;
+      while (tableCells(merged).length < expected && i + 1 < lines.length && /^\s*\|/.test(lines[i + 1]) && guard < 4) {
+        merged = mergeSplitTableRows(merged, lines[i + 1]);
+        i += 1;
+        guard += 1;
+      }
+      repaired.push(trimTableCellsToExpected(merged, expected));
+      i += 1;
+    }
+    continue;
+  }
+  return repaired.join('\n');
+}
+
+function isPotentialTableHeader(lines, idx) {
+  return idx + 1 < lines.length && /^\s*\|.*\|\s*$/.test(lines[idx]) && /^\s*\|?\s*:?-{2,}:?\s*(\|\s*:?-{2,}:?\s*)+\|?\s*$/.test(lines[idx + 1]);
+}
+
+function isSplitTableHeader(lines, idx) {
+  return idx + 2 < lines.length && /^\s*\|.*\|?\s*$/.test(lines[idx]) && /^\s*\|.*\|\s*$/.test(lines[idx + 1]) && /^\s*\|?\s*:?-{2,}:?\s*(\|\s*:?-{2,}:?\s*)+\|?\s*$/.test(lines[idx + 2]);
+}
+
+function normalizeTableSeparator(line, expected) {
+  var cells = tableCells(line);
+  while (cells.length < expected) cells.push('---');
+  return '| ' + cells.slice(0, expected).map(function(cell) { return /^:?-{2,}:?$/.test(cell) ? cell : '---'; }).join(' | ') + ' |';
+}
+
+function mergeSplitTableRows(left, right) {
+  var a = tableCells(left);
+  var b = tableCells(right);
+  if (!a.length) return right;
+  a[a.length - 1] = (a[a.length - 1] + ' ' + (b.shift() || '')).trim();
+  return '| ' + a.concat(b).join(' | ') + ' |';
+}
+
+function trimTableCellsToExpected(line, expected) {
+  var cells = tableCells(line);
+  while (cells.length < expected) cells.push('');
+  return '| ' + cells.slice(0, expected).join(' | ') + ' |';
 }
 
 export function fallbackMarkdown(text) {

public/js/clinicalAssistant.js

@@ -20,6 +20,7 @@ import { escapeAttr, escapeHtml, renderAssistantMarkdown, stripSourcesSection }
   var lastGeneratedImageSrc = '';
   var exportCacheKey = '';
   var exportCacheItems = null;
+  var markdownRenderer = null;
 
   document.addEventListener('tabChanged', function (e) {
     if (e.detail && e.detail.tab === 'assistant') initIfNeeded();
@@ -143,7 +144,7 @@ import { escapeAttr, escapeHtml, renderAssistantMarkdown, stripSourcesSection }
     })
     .catch(function (err) {
       setBusy(false, 'Error', true);
-      replaceLoadingMessage(loading, 'I could not complete the assistant request. ' + err.message + '\n\nIf this is the first run, the backend `/api/clinical-assistant/chat` route still needs to be wired to direct MCP search.');
+      replaceLoadingMessage(loading, 'I could not complete the assistant request. ' + err.message + '\n\nThe indexed search service may be busy or temporarily unavailable. Please try again in a moment.');
       if (typeof showToast === 'function') showToast(err.message, 'error');
     });
   }
@@ -228,14 +229,30 @@ import { escapeAttr, escapeHtml, renderAssistantMarkdown, stripSourcesSection }
     return wrap;
   }
 
-  function renderMarkdown(md, sources) {
+  function renderMarkdown(md, sources, options) {
+    var opts = options || {};
     return renderAssistantMarkdown(md, sources || [], {
-      marked: window.marked,
+      markdownIt: getMarkdownRenderer(),
       katex: window.katex,
-      sanitize: sanitize
+      sanitize: sanitize,
+      citationLabel: opts.citationLabel
     });
   }
 
+  function getMarkdownRenderer() {
+    if (markdownRenderer) return markdownRenderer;
+    if (typeof window.markdownit === 'function') {
+      markdownRenderer = window.markdownit({
+        html: false,
+        linkify: true,
+        typographer: true,
+        breaks: true
+      });
+      return markdownRenderer;
+    }
+    return null;
+  }
+
   function renderSources(sources) {
     var wrap = document.getElementById('assistant-sources');
     if (!wrap) return;
@@ -508,32 +525,28 @@ import { escapeAttr, escapeHtml, renderAssistantMarkdown, stripSourcesSection }
     if (!lastAnswer) { if (typeof showToast === 'function') showToast('No answer to export', 'error'); return; }
     var exportItems = collectExportItems();
     var cacheKey = buildExportCacheKey(exportItems, lastGeneratedImageSrc);
+    var doc = openExportWindow();
+    if (!doc) { if (typeof showToast === 'function') showToast('Allow popups to export PDF', 'error'); return; }
     if (exportCacheKey === cacheKey && exportCacheItems) {
-      openPrintableChatExport(exportCacheItems, lastGeneratedImageSrc);
+      writePrintableChatExport(doc, exportCacheItems, lastGeneratedImageSrc);
       return;
     }
-    setBusy(true, 'Preparing PDF...');
+    exportCacheKey = cacheKey;
-    fetch('/api/clinical-assistant/export-summary', {
+    exportCacheItems = exportItems;
-      method: 'POST', headers: getAuthHeaders(), credentials: 'same-origin',
+    writePrintableChatExport(doc, exportItems, lastGeneratedImageSrc);
-      body: JSON.stringify({ items: exportItems })
-    })
-    .then(function (r) { return r.json().then(function (data) { data._status = r.status; return data; }); })
-    .then(function (data) {
-      setBusy(false, 'Ready');
-      var items = data.success && Array.isArray(data.items) && data.items.length ? data.items : exportItems;
-      exportCacheKey = cacheKey;
-      exportCacheItems = items;
-      openPrintableChatExport(items, lastGeneratedImageSrc);
-    })
-    .catch(function () {
-      setBusy(false, 'Ready');
-      openPrintableChatExport(exportItems, lastGeneratedImageSrc);
-    });
   }
 
-  function openPrintableChatExport(items, imageSrc) {
+  function openExportWindow() {
     var doc = window.open('', '_blank', 'width=900,height=1100');
-    if (!doc) { if (typeof showToast === 'function') showToast('Allow popups to export PDF', 'error'); return; }
+    if (!doc) return null;
+    doc.document.open();
+    doc.document.write('<!doctype html><html><head><title>Preparing Clinical Assistant Export</title><style>body{font-family:Arial,sans-serif;color:#111827;margin:36px;line-height:1.5}.spinner{width:18px;height:18px;border:3px solid #e5e7eb;border-top-color:#7c3aed;border-radius:50%;display:inline-block;vertical-align:middle;margin-right:8px;animation:spin 1s linear infinite}@keyframes spin{to{transform:rotate(360deg)}}</style></head><body><p><span class="spinner"></span>Preparing PDF export...</p></body></html>');
+    doc.document.close();
+    return doc;
+  }
+
+  function writePrintableChatExport(doc, items, imageSrc) {
+    if (!doc || doc.closed) return;
     items = Array.isArray(items) && items.length ? items : collectExportItems();
     var imageHtml = imageSrc ? '<h2>Generated Image</h2><div class="export-image"><img src="' + escapeAttr(imageSrc) + '" alt="Generated clinical visual"></div>' : '';
     var sections = items.map(function (item, idx) {
@@ -545,20 +558,24 @@ import { escapeAttr, escapeHtml, renderAssistantMarkdown, stripSourcesSection }
       return '<section class="export-section">' +
         '<h2>' + escapeHtml(heading) + '</h2>' +
         '<div class="question"><strong>Question:</strong> ' + escapeHtml(item.question || '') + '</div>' +
-        (summary ? '<h3>Summary</h3><div class="answer">' + renderMarkdown(summary, sources) + '</div>' : '') +
+        (summary ? '<h3>Summary</h3><div class="answer">' + renderMarkdown(summary, sources, { citationLabel: 'number' }) + '</div>' : '') +
-        '<h3>Full Generated Answer</h3><div class="answer full-answer">' + renderMarkdown(answer, sources) + '</div>' +
+        '<h3>Full Generated Answer</h3><div class="answer full-answer">' + renderMarkdown(answer, sources, { citationLabel: 'number' }) + '</div>' +
         (refs ? '<h3>References</h3><ol class="refs">' + refs + '</ol>' : '') +
         '</section>';
     }).join('');
     var html = '<!doctype html><html><head><title>Clinical Assistant Export</title>' +
-      '<style>body{font-family:Arial,sans-serif;color:#111827;line-height:1.55;margin:36px;max-width:820px}h1{font-size:22px;margin:0 0 4px}h2{font-size:17px;margin-top:26px;border-bottom:1px solid #e5e7eb;padding-bottom:4px}h3{font-size:14px;margin:16px 0 6px}.meta,.question{font-size:12px;color:#6b7280;margin-bottom:12px}.answer{font-size:13px}.export-section{break-inside:avoid-page;margin-top:20px}.full-answer{page-break-before:auto}.export-image img{max-width:100%;border:1px solid #e5e7eb;border-radius:10px}.refs{font-size:12px;padding-left:20px}.refs li{margin:6px 0}.assistant-cite{color:#4f46e5;text-decoration:none;font-weight:700}@media print{button{display:none}body{margin:24mm}}</style>' +
+      '<style>body{font-family:Arial,sans-serif;color:#111827;line-height:1.55;margin:36px;max-width:820px}h1{font-size:22px;margin:0 0 4px}h2{font-size:17px;margin-top:26px;border-bottom:1px solid #e5e7eb;padding-bottom:4px;break-after:avoid}h3{font-size:14px;margin:18px 0 8px;break-after:avoid}.meta,.question{font-size:12px;color:#6b7280;margin-bottom:12px}.answer{font-size:13px}.export-section{margin-top:20px;break-before:auto}.full-answer{page-break-before:auto}.export-image img{max-width:100%;border:1px solid #e5e7eb;border-radius:10px}.refs{font-size:12px;padding-left:20px;margin-top:8px;break-inside:auto}.refs li{margin:6px 0;break-inside:avoid}.assistant-cite{display:inline-flex;align-items:center;justify-content:center;min-width:16px;height:16px;padding:0 5px;margin:0 1px;border-radius:999px;background:#f3e8ff;color:#7c3aed;border:1px solid rgba(124,58,237,.22);font-size:9px;font-weight:800;line-height:16px;text-decoration:none;text-transform:uppercase;letter-spacing:.03em;vertical-align:baseline;white-space:nowrap;-webkit-print-color-adjust:exact;print-color-adjust:exact}.answer table{width:100%;border-collapse:collapse;table-layout:auto;margin:12px 0 18px;border:1px solid #e5e7eb;page-break-inside:auto}.answer th,.answer td{padding:7px 8px;border:1px solid #e5e7eb;text-align:left;vertical-align:top;word-break:normal;overflow-wrap:break-word}.answer th{background:#f9fafb;font-weight:700;-webkit-print-color-adjust:exact;print-color-adjust:exact}.answer th:last-child,.answer td:last-child{width:1%;white-space:nowrap}.answer tr{break-inside:avoid;page-break-inside:avoid}.answer thead{display:table-header-group}.answer tbody{display:table-row-group}.answer p{margin:8px 0}.answer ul,.answer ol{padding-left:20px}.answer li{margin:4px 0}@media print{button{display:none}body{margin:24mm}.export-section{break-inside:auto}.refs{break-before:avoid}}</style>' +
-      '</head><body><button onclick="window.print()" style="float:right;padding:8px 12px">Print / Save PDF</button><h1>Clinical Assistant Export</h1>' +
+      '</head><body><button id="assistant-export-print" type="button" style="float:right;padding:8px 12px">Print / Save PDF</button><h1>Clinical Assistant Export</h1>' +
       '<div class="meta">Export generated ' + escapeHtml(new Date().toLocaleString()) + '</div>' +
       imageHtml +
       sections + '</body></html>';
     doc.document.open();
     doc.document.write(html);
     doc.document.close();
+    try {
+      var printBtn = doc.document.getElementById('assistant-export-print');
+      if (printBtn) printBtn.addEventListener('click', function () { doc.focus(); doc.print(); });
+    } catch (e) {}
     setTimeout(function () { try { doc.focus(); doc.print(); } catch (e) {} }, 500);
   }
 

server.js

@@ -208,6 +208,11 @@ app.get(['/', '/index.html'], function(req, res) {
 app.get('/api/build', function(req, res) { res.json({ buildId: BUILD_ID }); });
 
 app.use(loggingMiddleware);
+app.use('/vendor/markdown-it', express.static(path.join(__dirname, 'node_modules', 'markdown-it', 'dist'), {
+  setHeaders: function(res) {
+    res.setHeader('Cache-Control', 'public, max-age=3600');
+  }
+}));
 app.use(express.static(path.join(__dirname, 'public'), {
   setHeaders: (res, filePath) => {
     if (filePath.endsWith('.html')) {

src/routes/clinicalAssistant.js

@@ -9,6 +9,7 @@ var express = require('express');
 var axios = require('axios');
 var fs = require('fs');
 var path = require('path');
+var { S3Client, GetObjectCommand } = require('@aws-sdk/client-s3');
 var router = express.Router();
 var db = require('../db/database');
 var { authMiddleware } = require('../middleware/auth');
@@ -16,12 +17,20 @@ var { callAI } = require('../utils/ai');
 var { gatewayUrl } = require('../utils/errors');
 var logger = require('../utils/logger');
 var cryptoUtil = require('../utils/crypto');
+var redisCache = require('../utils/redis');
 
 router.use(authMiddleware);
 
 var MCP_URLS = buildMcpUrls();
 var _lastGoodMcpUrl = MCP_URLS[0];
-var DEFAULT_BEHAVIOR = 'You are a concise pediatric clinical assistant. Use retrieved context only for factual claims. If the user input is a greeting or too vague, answer briefly and ask what they want to look up. Synthesize across sources, cite claims with numbered citations like [1], and list sources at the bottom by title/resource and page. Do not invent citations.';
+var MCP_INITIALIZE_TIMEOUT_MS = positiveInt(process.env.CLINICAL_ASSISTANT_MCP_INITIALIZE_TIMEOUT_MS, 30000);
+var MCP_REQUEST_TIMEOUT_MS = positiveInt(process.env.CLINICAL_ASSISTANT_MCP_REQUEST_TIMEOUT_MS, 90000);
+var MCP_SESSION_TTL_MS = positiveInt(process.env.CLINICAL_ASSISTANT_MCP_SESSION_TTL_MS, 10 * 60 * 1000);
+var _mcpSession = null;
+var _mcpSessionPromise = null;
+var _mcpCallQueue = Promise.resolve();
+var _mcpRequestId = 1;
+var DEFAULT_BEHAVIOR = 'You are a concise pediatric clinical assistant. Use retrieved context only for factual claims. If the user input is a greeting or too vague, answer briefly and ask what they want to look up. Synthesize across sources and cite factual claims with the exact provided source numbers like [1]. Do not invent, renumber, merge, or move citations.';
 var GREETING_RE = /^(hi|hello|hey|yo|good\s+(morning|afternoon|evening)|thanks|thank you|ok|okay|sup)[\s.!?]*$/i;
 var EXAMPLE_CACHE_MS = 10 * 60 * 1000;
 var _exampleCache = { expiresAt: 0, examples: [] };
@@ -30,6 +39,10 @@ var MAX_SAVED_CHAT_PAYLOAD = 250000;
 var MAX_SAVED_CHAT_TITLE = 160;
 var MCP_MULTIMODAL_IMAGE_ROOT = path.resolve(process.env.CLINICAL_ASSISTANT_MULTIMODAL_IMAGE_ROOT || '/app/mcp-data/multimodal-pages');
 var MCP_MULTIMODAL_INTERNAL_ROOT = path.resolve(process.env.CLINICAL_ASSISTANT_MULTIMODAL_INTERNAL_ROOT || '/app/data/multimodal-pages');
+var MULTIMODAL_S3_ENDPOINT = process.env.CLINICAL_ASSISTANT_MULTIMODAL_S3_ENDPOINT || '';
+var MULTIMODAL_S3_ACCESS_KEY = process.env.CLINICAL_ASSISTANT_MULTIMODAL_S3_ACCESS_KEY || '';
+var MULTIMODAL_S3_SECRET_KEY = process.env.CLINICAL_ASSISTANT_MULTIMODAL_S3_SECRET_KEY || '';
+var _s3Client = null;
 var MULTIMODAL_EMBEDDING_URL = process.env.CLINICAL_ASSISTANT_MULTIMODAL_EMBEDDING_URL || 'http://multimodal-embeddings:7999/embed';
 var VISUAL_CLASSIFIER_ENABLED = process.env.CLINICAL_ASSISTANT_VISUAL_CLASSIFIER !== 'false';
 var VISUAL_CLASSIFIER_LIMIT = 6;
@@ -58,49 +71,62 @@ var EXAMPLE_CANDIDATES = [
 ];
 var TOPIC_SUGGESTIONS = {
   asthma: [
-    'Management of acute asthma exacerbation by severity',
+    'How should acute pediatric asthma exacerbation severity guide SABA frequency, ipratropium, steroids, magnesium sulfate, and disposition?',
-    'When to give magnesium sulfate in status asthmaticus',
+    'When should magnesium sulfate, continuous albuterol, noninvasive ventilation, ICU transfer, or intubation be considered in status asthmaticus?',
-    'Bronchiolitis versus asthma in infants with wheeze',
+    'How can bronchiolitis, viral-induced wheeze, and early asthma be distinguished in infants and preschool children?',
-    'Discharge criteria after pediatric asthma exacerbation',
+    'What discharge criteria, observation period, relapse risks, and follow-up are recommended after an ED asthma exacerbation?',
-    'Controller therapy step-up after ED asthma visit'
+    'When should controller therapy be started or stepped up after an ED asthma visit?'
   ],
   bronchiolitis: [
-    'Supportive management of bronchiolitis',
+    'What supportive care, suctioning, hydration, oxygen targets, and feeding guidance are recommended for infant bronchiolitis?',
-    'When bronchodilator trial is appropriate in bronchiolitis',
+    'When is a bronchodilator trial reasonable in bronchiolitis, and when should it be stopped?',
-    'Admission and oxygen criteria for bronchiolitis',
+    'What apnea risk, work of breathing, oxygen saturation, hydration, and social factors support admission for bronchiolitis?',
-    'Bronchiolitis versus early asthma',
+    'How can bronchiolitis be distinguished from early asthma, pneumonia, cardiac disease, or foreign body aspiration?',
-    'High-flow nasal cannula use in bronchiolitis'
+    'When should high-flow nasal cannula, CPAP, ICU transfer, or escalation be considered in bronchiolitis?'
   ],
   fever: [
-    'Fever without source by age group',
+    'How should fever without source be evaluated by age group in neonates, young infants, and older children?',
-    'Febrile neonate initial workup and antibiotics',
+    'What cultures, inflammatory markers, LP decisions, empiric antibiotics, and disposition are recommended for febrile neonates?',
-    'Risk stratification for serious bacterial infection',
+    'Which clinical and laboratory features stratify risk for serious bacterial infection in febrile infants?',
-    'When to do lumbar puncture in febrile infants',
+    'When is lumbar puncture indicated or avoidable in febrile infants by age and risk category?',
-    'Fever in immunocompromised children'
+    'How should fever be approached in immunocompromised children, central lines, or incomplete immunization?'
   ],
   seizure: [
-    'Status epilepticus first-line management',
+    'What is the timed pediatric status epilepticus algorithm including benzodiazepine dosing and second-line choices?',
-    'Febrile seizure evaluation and counseling',
+    'How should simple versus complex febrile seizures be evaluated, treated, and explained to caregivers?',
-    'Second-line antiseizure medications in children',
+    'When should levetiracetam, fosphenytoin, phenobarbital, valproate, anesthetic infusion, or ICU transfer be used?',
-    'When neuroimaging is indicated after seizure',
+    'Which seizure presentations require neuroimaging, labs, toxicology, LP, EEG, or admission?',
-    'Seizure mimics in pediatrics'
+    'What common seizure mimics in children should be considered and how are they distinguished?'
   ],
   croup: [
-    'Croup severity scoring and treatment',
+    'How should croup severity guide dexamethasone, nebulized epinephrine, observation, and disposition?',
-    'When to use nebulized epinephrine for croup',
+    'When is nebulized epinephrine indicated for croup and how long should the child be observed afterward?',
-    'Dexamethasone dosing in croup',
+    'What dexamethasone dose and route are recommended for mild, moderate, and severe croup?',
-    'Observation after racemic epinephrine',
+    'What discharge, admission, ICU, and airway escalation criteria apply after croup treatment?',
-    'Differential diagnosis for stridor'
+    'What alternative diagnoses should be considered in a child with stridor or atypical croup?'
   ],
   dehydration: [
-    'Clinical assessment of pediatric dehydration',
+    'Which clinical signs best estimate mild, moderate, and severe dehydration in children?',
-    'Oral rehydration therapy protocol',
+    'What oral rehydration protocol, volumes, antiemetic use, and reassessment are recommended for gastroenteritis?',
-    'IV fluid bolus and maintenance strategy',
+    'When are IV boluses, maintenance fluids, deficit replacement, glucose, or electrolyte checks indicated?',
-    'Hypernatremic dehydration precautions',
+    'How should hypernatremic dehydration be recognized and corrected safely?',
-    'Discharge criteria after gastroenteritis'
+    'What discharge, admission, and follow-up criteria apply after pediatric gastroenteritis or dehydration?'
   ]
 };
 
+function positiveInt(value, fallback) {
+  var n = Number(value);
+  return Number.isFinite(n) && n > 0 ? Math.floor(n) : fallback;
+}
+
+if (process.env.CLINICAL_ASSISTANT_MCP_WARMUP !== 'false') {
+  setTimeout(function() {
+    getMcpSession().catch(function(e) {
+      console.warn('[clinical-assistant] MCP warmup skipped:', e.message);
+    });
+  }, positiveInt(process.env.CLINICAL_ASSISTANT_MCP_WARMUP_DELAY_MS, 5000));
+}
+
 router.get('/clinical-assistant/status', async function(req, res) {
   try {
     var chatModel = await getSetting('clinical_assistant.chat_model', '') || await getSetting('models.default', '');
@@ -133,10 +159,19 @@ router.get('/clinical-assistant/examples', async function(req, res) {
 
 router.get('/clinical-assistant/source-image/:token', async function(req, res) {
   try {
-    var imagePath = resolveMultimodalImagePath(req.params.token || '');
-    if (!imagePath) return res.status(404).send('Not found');
     res.set('Cache-Control', 'private, max-age=3600');
     res.type('png');
+    var raw = base64UrlDecode(req.params.token || '');
+    if (isS3Uri(raw)) {
+      var obj = await getS3Object(raw);
+      if (!obj) return res.status(404).send('Not found');
+      if (obj.Body && typeof obj.Body.pipe === 'function') return obj.Body.pipe(res);
+      var chunks = [];
+      for await (var chunk of obj.Body) chunks.push(chunk);
+      return res.send(Buffer.concat(chunks));
+    }
+    var imagePath = resolveRawMultimodalImagePath(raw);
+    if (!imagePath) return res.status(404).send('Not found');
     res.sendFile(imagePath);
   } catch (e) {
     console.warn('[clinical-assistant] source image rejected:', e.message);
@@ -234,8 +269,11 @@ router.post('/clinical-assistant/chat', async function(req, res) {
       });
     }
 
+    var history = Array.isArray(req.body.history) ? req.body.history.slice(-8) : [];
+    var contextualHistory = priorClinicalHistory(history, message);
+
     var suggestions = getTopicSuggestions(message);
-    if (suggestions.length > 0 && message.split(/\s+/).length < 4) {
+    if (!contextualHistory.length && suggestions.length > 0 && message.split(/\s+/).length < 4) {
       return res.json({
         success: true,
         answer: buildSuggestionAnswer(message, suggestions),
@@ -246,7 +284,6 @@ router.post('/clinical-assistant/chat', async function(req, res) {
       });
     }
 
-    var history = Array.isArray(req.body.history) ? req.body.history.slice(-8) : [];
     var searchQuery = await rewriteSearchQuery(message, history, chatModel).catch(function(e) {
       console.warn('[clinical-assistant] query rewrite skipped:', e.message);
       return message;
@@ -268,6 +305,11 @@ router.post('/clinical-assistant/chat', async function(req, res) {
       normalizeMcpMultimodalResponse(multimodalResponse)
     );
     var rawResults = rawTextResults.concat(rawMultimodalResults);
+    console.info('[clinical-assistant] retrieval counts:', {
+      text: rawTextResults.length,
+      multimodal: rawMultimodalResults.length,
+      query: searchQuery
+    });
     var visualSlots = rawMultimodalResults.length ? Math.min(2, Math.max(1, Math.floor(searchLimit / 4))) : 0;
     var textSlots = searchLimit - visualSlots;
     var sources = dedupeSources(
@@ -298,9 +340,6 @@ router.post('/clinical-assistant/chat', async function(req, res) {
       maxTokens: 1800
     });
     var answer = stripModelSourcesSection(String(ai.content || '').trim());
-    var normalized = normalizeCitationOrder(answer, sources);
-    answer = normalized.answer;
-    sources = normalized.sources;
 
     logger.audit(req.user.id, 'clinical_assistant_query', 'Clinical assistant query', req, {
       category: 'clinical', model: ai.model || chatModel, duration: Date.now() - started
@@ -390,6 +429,9 @@ async function rewriteSearchQuery(message, history, chatModel) {
   }
   if (!history.length || !needsContextualRewrite(message)) return message;
 
+  var deterministic = deterministicFollowupQuery(message, history);
+  if (deterministic) return deterministic;
+
   var hist = history.map(function(m) {
     return m.role.toUpperCase() + ': ' + String(m.content).substring(0, 900);
   }).join('\n');
@@ -420,6 +462,35 @@ function needsContextualRewrite(message) {
   return words.length <= 8 || /\b(it|this|that|they|them|he|she|dose|dosing|how much|what about|next|admit|discharge|criteria|side effects?|contraindications?|monitor|monitoring)\b/i.test(text);
 }
 
+function priorClinicalHistory(history, message) {
+  var latest = String(message || '').trim();
+  return (Array.isArray(history) ? history : []).filter(function(m) {
+    return m && (m.role === 'user' || m.role === 'assistant') && m.content && String(m.content).trim() !== latest;
+  });
+}
+
+function deterministicFollowupQuery(message, history) {
+  var text = String(message || '').trim().toLowerCase();
+  if (!/^(dose|dosing|what dose|dose\?|how much|med dose|medication dose)$/i.test(text)) return '';
+  var prior = previousUserQuestion(history) || previousAssistantTopic(history);
+  if (!prior) return '';
+  return 'medication dosing and immediate treatment details for: ' + prior;
+}
+
+function previousUserQuestion(history) {
+  for (var i = history.length - 1; i >= 0; i--) {
+    if (history[i] && history[i].role === 'user' && history[i].content) return clip(history[i].content, 300);
+  }
+  return '';
+}
+
+function previousAssistantTopic(history) {
+  for (var i = history.length - 1; i >= 0; i--) {
+    if (history[i] && history[i].role === 'assistant' && history[i].content) return clip(history[i].content, 300);
+  }
+  return '';
+}
+
 async function summarizeExportItems(items) {
   var chatModel = await getSetting('clinical_assistant.chat_model', '') || await getSetting('models.default', '');
   var clean = items.slice(0, 20).map(function(item, idx) {
@@ -498,16 +569,67 @@ async function multimodalSearch(query, opts) {
 
 async function indexedTopicSuggestions(limit) {
   return callMcpTool('nc_indexed_topic_suggestions', {
-    limit: limit || 9,
+    limit: limit || 12,
-    sample_size: 900,
+    sample_size: 1500,
     doc_type: 'file'
   });
 }
 
 async function callMcpTool(name, args) {
+  var queued = _mcpCallQueue.then(function() {
+    return callMcpToolUnlocked(name, args);
+  });
+  _mcpCallQueue = queued.catch(function() {});
+  return queued;
+}
+
+async function callMcpToolUnlocked(name, args) {
+  var session = await getMcpSession();
+  var payload = {
+    jsonrpc: '2.0',
+    id: nextMcpRequestId(),
+    method: 'tools/call',
+    params: {
+      name: name,
+      arguments: args
+    }
+  };
+  var search;
+  try {
+    search = await mcpRequest(payload, session.sessionId, session.mcpUrl);
+  } catch (e) {
+    if (!isInvalidMcpSessionError(e)) throw e;
+    _mcpSession = null;
+    session = await getMcpSession();
+    payload.id = nextMcpRequestId();
+    search = await mcpRequest(payload, session.sessionId, session.mcpUrl);
+  }
+  return search.result || search;
+}
+
+function nextMcpRequestId() {
+  _mcpRequestId += 1;
+  if (_mcpRequestId > 1000000000) _mcpRequestId = 2;
+  return _mcpRequestId;
+}
+
+async function getMcpSession() {
+  var now = Date.now();
+  if (_mcpSession && _mcpSession.sessionId && _mcpSession.expiresAt > now) return _mcpSession;
+  if (_mcpSessionPromise) return _mcpSessionPromise;
+  _mcpSessionPromise = initializeMcpSession().then(function(session) {
+    _mcpSession = session;
+    return session;
+  }).finally(function() {
+    _mcpSessionPromise = null;
+  });
+  return _mcpSessionPromise;
+}
+
+async function initializeMcpSession() {
   var session = await mcpRequest({
     jsonrpc: '2.0',
-    id: 1,
+    id: nextMcpRequestId(),
     method: 'initialize',
     params: {
       protocolVersion: '2024-11-05',
@@ -515,16 +637,8 @@ async function callMcpTool(name, args) {
       clientInfo: { name: 'ped-ai-clinical-assistant', version: '1.0.0' }
     }
   });
-  var search = await mcpRequest({
+  session.expiresAt = Date.now() + MCP_SESSION_TTL_MS;
-    jsonrpc: '2.0',
+  return session;
-    id: 2,
-    method: 'tools/call',
-    params: {
-      name: name,
-      arguments: args
-    }
-  }, session.sessionId, session.mcpUrl);
-  return search.result || search;
 }
 
 async function mcpRequest(payload, sessionId, preferredUrl) {
@@ -551,7 +665,7 @@ async function postMcpWithRetry(payload, headers, preferredUrl) {
       try {
         var resp = await axios.post(url, payload, {
           headers: headers,
-          timeout: isInitialize ? 8000 : 90000,
+          timeout: isInitialize ? MCP_INITIALIZE_TIMEOUT_MS : MCP_REQUEST_TIMEOUT_MS,
           responseType: 'text',
           transformResponse: [function(data) { return data; }]
         });
@@ -582,6 +696,12 @@ function isTransientMcpError(e) {
   return code === 'ECONNREFUSED' || code === 'ECONNRESET' || code === 'ETIMEDOUT' || status === 502 || status === 503 || status === 504;
 }
 
+function isInvalidMcpSessionError(e) {
+  var status = e && e.response && e.response.status;
+  var msg = String(e && e.message || '');
+  return status === 400 || status === 404 || status === 410 || /session|mcp-session-id/i.test(msg);
+}
+
 async function getMcpHealth() {
   var results = [];
   var urls = orderedMcpUrls();
@@ -707,6 +827,9 @@ function normalizeMcpMultimodalResponse(result) {
       visual_caption: caption,
       visual_labels: labels,
       visual_caption_source: r.visual_caption_source || '',
+      is_cover_page: Boolean(r.is_cover_page || r.isCoverPage),
+      is_title_page: Boolean(r.is_title_page || r.isTitlePage),
+      reject_for_visual_search: Boolean(r.reject_for_visual_search || r.rejectForVisualSearch),
       excerpt: excerptParts.length ? '[Page-image match] ' + excerptParts.join('\n') : '[Page-image match] Rendered PDF page matched the visual/text query.',
       score: r.score,
       image_path_internal: r.image_path || '',
@@ -718,17 +841,40 @@ function normalizeMcpMultimodalResponse(result) {
 }
 
 function dedupeSources(results) {
-  var seen = new Set();
+  var seen = new Map();
   var out = [];
   results.forEach(function(r) {
-    var key = [r.title, r.page || '', r.chunk_index || ''].join('|');
+    var key = sourceDedupeKey(r);
-    if (seen.has(key)) return;
+    var existingIndex = seen.get(key);
-    seen.add(key);
+    if (existingIndex != null) {
+      out[existingIndex] = mergeDuplicateSource(out[existingIndex], r);
+      return;
+    }
+    seen.set(key, out.length);
     out.push(Object.assign({}, r, { number: out.length + 1 }));
   });
   return out;
 }
 
+function sourceDedupeKey(source) {
+  var title = cleanTitle(source && source.title || '').toLowerCase();
+  var page = source && source.page ? String(source.page) : '';
+  var kind = source && source.source_type ? source.source_type : 'text';
+  if (title && page) return [kind, title, page].join('|');
+  return [kind, title, source && source.id || source && source.chunk_index || ''].join('|');
+}
+
+function mergeDuplicateSource(existing, duplicate) {
+  var merged = Object.assign({}, existing);
+  var existingExcerpt = cleanSourceExcerpt(existing.excerpt || '');
+  var duplicateExcerpt = cleanSourceExcerpt(duplicate.excerpt || '');
+  if (duplicateExcerpt && existingExcerpt.indexOf(duplicateExcerpt.slice(0, 160)) === -1) {
+    merged.excerpt = clip([existingExcerpt, duplicateExcerpt].filter(Boolean).join('\n'), 1800);
+  }
+  merged.score = Math.max(Number(existing.score) || 0, Number(duplicate.score) || 0) || existing.score || duplicate.score;
+  return merged;
+}
+
 function formatSourcesForPrompt(sources) {
   return sources.map(function(s) {
     var label = s.source_type === 'multimodal_page' ? ' [visual PDF page match]' : '';
@@ -737,7 +883,7 @@ function formatSourcesForPrompt(sources) {
 }
 
 function buildSystemPrompt(behavior) {
-  return behavior + '\n\nRules:\n- Answer only the user question; do not dump unrelated textbook content.\n- Use numbered citations [1], [2] for factual claims, matching the provided source numbers.\n- If sources disagree or are insufficient, say so.\n- Do not cite a source number that is not provided.\n- Keep the main answer concise and clinically useful.\n- Use clear markdown with headings, bullets, and tables when useful.\n- Do not add a final Sources or References section; the UI displays all retrieved sources separately.\n- Do not add generic disclaimers about clinician judgment.';
+  return behavior + '\n\nRules:\n- Answer only the user question; do not dump unrelated textbook content.\n- Use the exact source numbers from the retrieved indexed sources; do not renumber citations for order or style.\n- Cite factual claims immediately with numbered citations like [1] or [1, 3].\n- Every clinical recommendation, dose, threshold, lab value, statistic, comparison, contraindication, red flag, and table row must include its own supporting citation.\n- Do not leave a paragraph, bullet, or table row with multiple factual claims supported only by an uncited heading.\n- If a claim is not directly supported by retrieved sources, omit it or state that the indexed sources are insufficient.\n- Do not cite a source number that is not provided.\n- If sources disagree or are insufficient, say so.\n- Keep the main answer concise and clinically useful.\n- Use clear markdown with headings, bullets, and tables when useful.\n- Do not add a final Sources or References section; the UI displays all retrieved sources separately.\n- Do not add generic disclaimers about clinician judgment.';
 }
 
 function buildUserPrompt(question, context, history, searchQuery) {
@@ -754,44 +900,6 @@ function stripModelSourcesSection(answer) {
     .trim();
 }
 
-function normalizeCitationOrder(answer, sources) {
-  sources = Array.isArray(sources) ? sources : [];
-  var used = [];
-  var oldToNew = {};
-  var re = /\[((?:\d+\s*,\s*)*\d+)\]/g;
-  var m;
-  while ((m = re.exec(answer))) {
-    parseCitationCluster(m[1]).forEach(function(oldNum) {
-      if (!sources[oldNum - 1] || oldToNew[oldNum]) return;
-      oldToNew[oldNum] = used.length + 1;
-      used.push(oldNum);
-    });
-  }
-
-  var reordered = [];
-  used.forEach(function(oldNum) { reordered.push(sources[oldNum - 1]); });
-  sources.forEach(function(source, idx) {
-    if (used.indexOf(idx + 1) === -1) reordered.push(source);
-  });
-  reordered = reordered.map(function(source, idx) {
-    return Object.assign({}, source, { number: idx + 1 });
-  });
-
-  var rewritten = answer.replace(/\[((?:\d+\s*,\s*)*\d+)\]/g, function(match, cluster) {
-    var oldNums = parseCitationCluster(cluster);
-    var nums = oldNums.map(function(oldNum) { return oldToNew[oldNum]; });
-    if (!nums.length || nums.some(function(n) { return !n; })) return match;
-    nums = Array.from(new Set(nums)).sort(function(a, b) { return a - b; });
-    return '[' + nums.join(', ') + ']';
-  });
-
-  return { answer: rewritten, sources: reordered };
-}
-
-function parseCitationCluster(cluster) {
-  return String(cluster || '').split(',').map(function(n) { return Number(n.trim()); }).filter(function(n) { return Number.isInteger(n) && n > 0; });
-}
-
 function isVisualSourceQuery(query) {
   return visualIntent(query).wanted.length > 0;
 }
@@ -813,6 +921,8 @@ async function classifyAndRerankMultimodalResults(query, results) {
   results = Array.isArray(results) ? results : [];
   if (!results.length) return [];
   var candidates = results.slice(0, VISUAL_CLASSIFIER_LIMIT);
+  candidates = candidates.filter(function(candidate) { return !shouldRejectVisualSource(query, candidate); });
+  if (!candidates.length) return [];
   if (!VISUAL_CLASSIFIER_ENABLED) return selectMultimodalResults(query, candidates);
   var intent = visualIntent(query);
   var classified = [];
@@ -842,6 +952,8 @@ async function classifyAndRerankMultimodalResults(query, results) {
 function selectMultimodalResults(query, results) {
   results = Array.isArray(results) ? results : [];
   if (!results.length) return [];
+  results = results.filter(function(r) { return !shouldRejectVisualSource(query, r); });
+  if (!results.length) return [];
   if (!isRadiologyQuery(query)) return results.filter(function(r) { return !looksLikeTextOnlyPage(r); });
   var radiologyTerms = /\b(radiology|radiologic|radiograph|x-?ray|cxr|chest\s*(film|x-?ray|radiograph)|imaging|ultrasound|ct|mri|scan|film|pneumonia|bronchiolitis|lung|airway|hyperinflation|infiltrate|consolidation|atelectasis)\b/i;
   return results.filter(function(r) {
@@ -909,10 +1021,33 @@ function visualMetadataScore(query, source) {
   if (intent.wanted.indexOf('diagram') !== -1 && /\b(figure|diagram|algorithm|flowchart|pathway|chart|illustration|infographic)\b/i.test(haystack)) score += 0.12;
   if (intent.wanted.indexOf('photo') !== -1 && /\b(photo|photograph|skin|rash|lesion|wound|gross|microscopy|histology)\b/i.test(haystack)) score += 0.12;
   if (/\b(pneumonia|bronchiolitis|lung|airway|hyperinflation|infiltrate|consolidation|atelectasis)\b/i.test(haystack)) score += 0.06;
+  if (looksLikeFrontMatterPage(source)) score -= 0.5;
   if (looksLikeTextOnlyPage(source)) score -= 0.18;
   return score;
 }
 
+function shouldRejectVisualSource(query, source) {
+  if (!source) return false;
+  if (allowsFrontMatterQuery(query)) return false;
+  return Boolean(source.reject_for_visual_search || source.is_cover_page || source.is_title_page || looksLikeFrontMatterPage(source));
+}
+
+function allowsFrontMatterQuery(query) {
+  return /\b(cover|front cover|title page|copyright|table of contents|contents|preface|foreword|publisher|isbn)\b/i.test(String(query || ''));
+}
+
+function looksLikeFrontMatterPage(source) {
+  var page = Number(source && source.page) || 0;
+  var pageCount = Number(source && source.page_count) || 0;
+  var earlyLimit = Math.min(8, Math.max(2, pageCount || 8));
+  if (!page || page > earlyLimit) return false;
+  var haystack = [source.title, source.excerpt, source.visual_caption, (source.visual_labels || []).join(' '), source.file_path].filter(Boolean).join(' ');
+  var hasVisualSignal = /\b(figure|fig\.?|radiograph|x-?ray|cxr|ultrasound|ct|mri|photograph|photo|image|diagram|flowchart|algorithm|histology|microscopy|gross pathology)\b/i.test(haystack);
+  if (hasVisualSignal) return false;
+  var frontMatterSignal = /\b(cover|front cover|title page|copyright|all rights reserved|isbn|library of congress|table of contents|contents|preface|foreword|dedication|contributors?|textbook of|manual of|review of|board review|edition|authors?|editor|publisher)\b/i.test(haystack);
+  return frontMatterSignal || page <= 2;
+}
+
 function looksLikeTextOnlyPage(source) {
   var text = String(source && source.excerpt || '');
   return text.length > 900 && !/\b(figure|image|radiograph|x-?ray|cxr|ultrasound|ct|mri|scan|film|diagram|illustration)\b/i.test(text);
@@ -960,6 +1095,38 @@ function resolveRawMultimodalImagePath(raw) {
   return servedPath;
 }
 
+function isS3Uri(value) {
+  return /^s3:\/\/[^/]+\/.+/.test(String(value || ''));
+}
+
+function parseS3Uri(uri) {
+  var m = String(uri || '').match(/^s3:\/\/([^/]+)\/(.+)$/);
+  if (!m) return null;
+  return { bucket: m[1], key: m[2] };
+}
+
+function getS3Client() {
+  if (_s3Client) return _s3Client;
+  if (!MULTIMODAL_S3_ENDPOINT || !MULTIMODAL_S3_ACCESS_KEY || !MULTIMODAL_S3_SECRET_KEY) return null;
+  _s3Client = new S3Client({
+    endpoint: MULTIMODAL_S3_ENDPOINT,
+    region: process.env.CLINICAL_ASSISTANT_MULTIMODAL_S3_REGION || 'us-east-1',
+    forcePathStyle: true,
+    credentials: {
+      accessKeyId: MULTIMODAL_S3_ACCESS_KEY,
+      secretAccessKey: MULTIMODAL_S3_SECRET_KEY
+    }
+  });
+  return _s3Client;
+}
+
+async function getS3Object(uri) {
+  var parsed = parseS3Uri(uri);
+  var client = getS3Client();
+  if (!parsed || !client) return null;
+  return client.send(new GetObjectCommand({ Bucket: parsed.bucket, Key: parsed.key }));
+}
+
 function sanitizeSourcesForClient(sources) {
   return (Array.isArray(sources) ? sources : []).map(function(source) {
     var out = Object.assign({}, source);
@@ -1072,6 +1239,11 @@ function cleanExportHeading(heading, idx) {
 async function getAvailableExamples() {
   var now = Date.now();
   if (_exampleCache.expiresAt > now && _exampleCache.examples.length) return _exampleCache.examples;
+  var cached = await redisCache.getJson('clinical-assistant:examples:v1').catch(function() { return null; });
+  if (cached && Array.isArray(cached.examples) && cached.examples.length) {
+    _exampleCache = { expiresAt: now + EXAMPLE_CACHE_MS, examples: cached.examples };
+    return cached.examples;
+  }
 
   var indexedExamples = await getIndexedTopicExamples().catch(function(e) {
     console.warn('[clinical-assistant] indexed topic suggestions skipped:', e.message);
@@ -1079,6 +1251,7 @@ async function getAvailableExamples() {
   });
   if (indexedExamples.length >= 3) {
     _exampleCache = { expiresAt: now + EXAMPLE_CACHE_MS, examples: indexedExamples };
+    redisCache.setJson('clinical-assistant:examples:v1', { examples: indexedExamples }, 1800).catch(function() {});
     return indexedExamples;
   }
 
@@ -1110,11 +1283,12 @@ async function getAvailableExamples() {
     expiresAt: now + EXAMPLE_CACHE_MS,
     examples: examples
   };
+  redisCache.setJson('clinical-assistant:examples:v1', { examples: examples }, 1800).catch(function() {});
   return examples;
 }
 
 async function getIndexedTopicExamples() {
-  var response = await indexedTopicSuggestions(9);
+  var response = await indexedTopicSuggestions(12);
   var data = response && (response.structuredContent || response.data || response);
   if ((!data || !Array.isArray(data.suggestions)) && response && Array.isArray(response.content)) {
     for (var i = 0; i < response.content.length; i++) {
@@ -1128,7 +1302,7 @@ async function getIndexedTopicExamples() {
     }
   }
   if (!data || !Array.isArray(data.suggestions)) return [];
-  return data.suggestions.slice(0, 9).map(function(item) {
+  return data.suggestions.slice(0, 12).map(function(item) {
     return {
       label: item.label || 'Indexed topic',
       prompt: item.prompt || '',
@@ -1148,10 +1322,11 @@ async function generateImage(prompt, model) {
   if (!process.env.LITELLM_API_BASE) throw new Error('LiteLLM is required for image generation');
   var headers = { 'Content-Type': 'application/json' };
   if (process.env.LITELLM_API_KEY) headers.Authorization = 'Bearer ' + process.env.LITELLM_API_KEY;
+  var renderedPrompt = imagePromptForCanvas(prompt);
   var size = process.env.CLINICAL_ASSISTANT_IMAGE_SIZE || 'auto';
-  var resp = await generateImageRequest(model, imagePromptForCanvas(prompt), size, headers).catch(async function(e) {
+  var resp = await generateImageRequest(model, renderedPrompt, size, headers).catch(async function(e) {
     if (!isInvalidImageSizeError(e) || size === '1024x1024') throw e;
-    return generateImageRequest(model, imagePromptForCanvas(prompt), '1024x1024', headers);
+    return generateImageRequest(model, renderedPrompt, '1024x1024', headers);
   });
   var item = resp.data && resp.data.data && resp.data.data[0] ? resp.data.data[0] : {};
   return { imageUrl: item.url || null, base64: item.b64_json || null, raw: (!item.url && !item.b64_json) ? resp.data : undefined };
@@ -1167,12 +1342,12 @@ function generateImageRequest(model, prompt, size, headers) {
 
 function imagePromptForCanvas(prompt) {
   var text = String(prompt || '');
-  var guidance = ' Keep all text and boxes fully inside the canvas with generous margins. Use fewer words per box, large readable type, and avoid cropping at edges.';
+  var guidance = ' Compose as a single complete medical teaching poster. Keep every element fully inside the canvas with a 10% safe margin on all sides. Do not crop boxes, arrows, labels, legends, or body parts. Use fewer words per box, large readable type, and generous spacing.';
   if (/\b(flow\s*chart|flowchart|algorithm|pathway|timeline|vertical|stepwise|decision\s*tree|age\s*group|0-21|22-28|29-60)\b/i.test(text)) {
-    guidance += ' Prefer a tall portrait canvas with top-to-bottom flow and ample spacing between decision nodes.';
+    guidance += ' Use a tall portrait layout with top-to-bottom flow, no more than 6-8 main nodes, and ample spacing between decision nodes.';
   }
   if (/\b(table|matrix|comparison|wide|landscape|side-by-side)\b/i.test(text)) {
-    guidance += ' Prefer a wide landscape canvas with columns and ample horizontal spacing.';
+    guidance += ' Use a wide landscape layout with compact columns, ample horizontal spacing, and no text near the edges.';
   }
   return text.trim() + guidance;
 }
@@ -1233,18 +1408,18 @@ function getTopicSuggestions(message) {
   }
   if (normalized.split(/\s+/).length <= 2) {
     return [
-      'Management of ' + normalized,
+      'What initial ED evaluation, severity assessment, and immediate stabilization steps are recommended for pediatric ' + normalized + '?',
-      'Red flags and differential diagnosis for ' + normalized,
+      'Which red flags, differential diagnoses, and complications should not be missed in pediatric ' + normalized + '?',
-      'Initial ED evaluation for ' + normalized,
+      'What treatment escalation, medication dosing, and monitoring are recommended for pediatric ' + normalized + '?',
-      'Admission versus discharge criteria for ' + normalized,
+      'What admission, discharge, observation, and follow-up criteria are recommended for pediatric ' + normalized + '?',
-      'Medication dosing and escalation for ' + normalized
+      'How do recommendations differ by age group, severity, comorbidity, or high-risk features in pediatric ' + normalized + '?'
     ];
   }
   return [];
 }
 
 function buildSuggestionAnswer(topic, suggestions) {
-  return 'I can look up **' + topic + '**. Pick a focused question so I can retrieve the most relevant cited pages:\n\n' +
+  return 'I can look up **' + topic + '**. Pick a specific clinical question so I retrieve the right cited pages instead of giving a broad summary:\n\n' +
     suggestions.map(function(s) { return '- ' + s; }).join('\n') +
     '\n\nOr type your own specific question, for example: "management of acute asthma exacerbation in a 6-year-old".';
 }

src/utils/redis.js

@@ -0,0 +1,41 @@
+var { createClient } = require('redis');
+
+var client = null;
+var connecting = null;
+
+async function getRedis() {
+  var url = process.env.REDIS_URL;
+  if (!url) return null;
+  if (client && client.isOpen) return client;
+  if (connecting) return connecting;
+  client = createClient({ url: url });
+  client.on('error', function(err) {
+    console.warn('[redis]', err.message);
+  });
+  connecting = client.connect().then(function() {
+    connecting = null;
+    return client;
+  }).catch(function(err) {
+    connecting = null;
+    console.warn('[redis] unavailable:', err.message);
+    return null;
+  });
+  return connecting;
+}
+
+async function getJson(key) {
+  var redis = await getRedis();
+  if (!redis) return null;
+  var value = await redis.get(key);
+  if (!value) return null;
+  try { return JSON.parse(value); } catch (e) { return null; }
+}
+
+async function setJson(key, value, ttlSeconds) {
+  var redis = await getRedis();
+  if (!redis) return false;
+  await redis.set(key, JSON.stringify(value), { EX: ttlSeconds });
+  return true;
+}
+
+module.exports = { getRedis, getJson, setJson };

test/assistant-citations.test.js

@@ -2,6 +2,7 @@ const { test } = require('node:test');
 const assert = require('node:assert/strict');
 const fs = require('node:fs/promises');
 const path = require('node:path');
+const MarkdownIt = require('markdown-it');
 
 let modulePromise;
 
@@ -24,8 +25,16 @@ test('renders citation clusters as links to matching source cards', async () =>
   const html = renderAssistantMarkdown('Give magnesium for severe exacerbation [1, 2].', sources);
   assert.match(html, /href="#assistant-source-1"/);
   assert.match(html, /href="#assistant-source-2"/);
-  assert.match(html, /title="Nelson Textbook of Pediatrics"/);
+  assert.match(html, /title="Source 1: Nelson Textbook of Pediatrics"/);
-  assert.match(html, /\[<a class="assistant-cite"[^>]*>1<\/a>, <a class="assistant-cite"[^>]*>2<\/a>\]/);
+  assert.match(html, /data-source-number="1"/);
+  assert.match(html, /data-source-number="2"/);
+  assert.match(html, /<a class="assistant-cite"[^>]*>src<\/a> <a class="assistant-cite"[^>]*>src<\/a>/);
+});
+
+test('can render citation labels as numbers for PDF export', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const html = renderAssistantMarkdown('Give magnesium for severe exacerbation [1, 2].', sources, { citationLabel: 'number' });
+  assert.match(html, /<a class="assistant-cite"[^>]*>1<\/a> <a class="assistant-cite"[^>]*>2<\/a>/);
 });
 
 test('leaves unknown citation clusters untouched rather than guessing', async () => {
@@ -38,9 +47,9 @@ test('leaves unknown citation clusters untouched rather than guessing', async ()
 test('does not merge separate citations across separate claims', async () => {
   const { renderAssistantMarkdown } = await loadCitationModule();
   const html = renderAssistantMarkdown('Use oxygen [1]. Give bronchodilator [2].', sources);
-  assert.match(html, /oxygen \[<a class="assistant-cite"[^>]*>1<\/a>\]/);
+  assert.match(html, /oxygen <a class="assistant-cite"[^>]*data-source-number="1"[^>]*>src<\/a>/);
-  assert.match(html, /bronchodilator \[<a class="assistant-cite"[^>]*>2<\/a>\]/);
+  assert.match(html, /bronchodilator <a class="assistant-cite"[^>]*data-source-number="2"[^>]*>src<\/a>/);
-  assert.doesNotMatch(html, />1<\/a>, <a class="assistant-cite"[^>]*>2<\/a>/);
+  assert.doesNotMatch(html, /data-source-number="1"[^>]*>src<\/a><a class="assistant-cite"[^>]*data-source-number="2"/);
 });
 
 test('sorts adjacent citation tokens into one safe Vancouver cluster', async () => {
@@ -48,7 +57,7 @@ test('sorts adjacent citation tokens into one safe Vancouver cluster', async ()
   const html = renderAssistantMarkdown('Deteriorating course [1][4][2][3].', [
     { title: 'A' }, { title: 'B' }, { title: 'C' }, { title: 'D' }
   ]);
-  assert.match(html, />1<\/a>, <a class="assistant-cite"[^>]*>2<\/a>, <a class="assistant-cite"[^>]*>3<\/a>, <a class="assistant-cite"[^>]*>4<\/a>/);
+  assert.match(html, /data-source-number="1"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="2"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="3"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="4"[^>]*>src<\/a>/);
   assert.doesNotMatch(html, /\]<span|\]\[/);
 });
 
@@ -57,7 +66,7 @@ test('repairs a clearly adjacent trailing citation missing its closing bracket',
   const html = renderAssistantMarkdown('Deteriorating course [1][4][2][3', [
     { title: 'A' }, { title: 'B' }, { title: 'C' }, { title: 'D' }
   ]);
-  assert.match(html, />1<\/a>, <a class="assistant-cite"[^>]*>2<\/a>, <a class="assistant-cite"[^>]*>3<\/a>, <a class="assistant-cite"[^>]*>4<\/a>/);
+  assert.match(html, /data-source-number="1"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="2"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="3"[^>]*>src<\/a> <a class="assistant-cite"[^>]*data-source-number="4"[^>]*>src<\/a>/);
 });
 
 test('does not normalize adjacent citations if any source number is unknown', async () => {
@@ -70,7 +79,7 @@ test('does not normalize adjacent citations if any source number is unknown', as
 test('escapes source titles inside citation link titles', async () => {
   const { renderAssistantMarkdown } = await loadCitationModule();
   const html = renderAssistantMarkdown('Unsafe title [1].', [{ title: 'Bad "Title" <script>' }]);
-  assert.match(html, /title="Bad &quot;Title&quot; &lt;script&gt;"/);
+  assert.match(html, /title="Source 1: Bad &quot;Title&quot; &lt;script&gt;"/);
   assert.doesNotMatch(html, /<script>/);
 });
 
@@ -120,9 +129,76 @@ test('repairs smashed admission bullet list after citations', async () => {
   assert.doesNotMatch(html, /\]-/);
 });
 
+test('repairs smashed head injury red flag bullets after citation clusters', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const html = renderAssistantMarkdown('CT is indicated for: [1, 2, 3]- Focal neurologic deficits [1]- Signs of skull fracture [2]- Recurrent vomiting [3]', sources);
+  assert.match(html, /<li>Focal neurologic deficits/);
+  assert.match(html, /<li>Signs of skull fracture/);
+  assert.match(html, /<li>Recurrent vomiting/);
+  assert.doesNotMatch(html, /\]-/);
+});
+
 test('preserves code block contents without creating citation links inside code', async () => {
   const { renderAssistantMarkdown } = await loadCitationModule();
   const html = renderAssistantMarkdown('```js\nconst ref = "[1]";\n```', sources);
   assert.match(html, /<pre><code>const ref = &quot;\[1\]&quot;/);
   assert.doesNotMatch(html, /assistant-source-1/);
 });
+
+test('repairs model-split markdown tables before rendering', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const html = renderAssistantMarkdown('Summary Table\n| Indication for Use | Dose (IV) | Max Dose\n\n| Infusion Time | Monitoring/Precautions |\n|-----------------------------------------|----------------------------|----------|--------------|---------------------------------------|\n| Severe exacerbation unresponsive to SABA/anticholinergic | 25-75 mg/kg | 2 g\n| 20 min | BP, reflexes, respiratory status[1, 2] |', sources);
+  assert.match(html, /<table>/);
+  assert.match(html, /Max Dose Infusion Time/);
+  assert.match(html, /2 g 20 min/);
+  assert.doesNotMatch(html, /<p>\| Infusion Time/);
+});
+
+test('breaks inline numbered clinical sections onto new lines', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const html = renderAssistantMarkdown('Monitor with serial abdominal exams [1]. 2. Imaging\nImmediate abdominal X-ray for obstruction [1, 2]. 3. Laboratory Studies\nAssess electrolytes if ill-appearing [3]. 4. Surgical Consultation\nUrgent pediatric surgical consultation [1].', sources);
+  assert.match(html, /2\. Imaging/);
+  assert.match(html, /3\. Laboratory Studies/);
+  assert.match(html, /4\. Surgical Consultation/);
+  assert.doesNotMatch(html, /exams[^<]*2\. Imaging/);
+  assert.doesNotMatch(html, /obstruction[^<]*3\. Laboratory Studies/);
+});
+
+test('strips orphan trailing markdown emphasis markers', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const html = renderAssistantMarkdown('Summary Table\n\nAge Group\tEmpiric Antibiotics\n<1 month\tAmpicillin + cefotaxime\n**', sources);
+  assert.match(html, /Summary Table/);
+  assert.doesNotMatch(html, /\*\*/);
+});
+
+test('uses markdown-it stack for GFM-style tables when provided', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const markdownIt = new MarkdownIt({ html: false, linkify: true, typographer: true, breaks: true });
+  const html = renderAssistantMarkdown('| Age | Antibiotics |\n|---|---|\n| <1 month | Ampicillin + cefotaxime [1] |', sources, { markdownIt });
+  assert.match(html, /<table>/);
+  assert.match(html, /<td>&lt;1 month<\/td>/);
+  assert.match(html, /assistant-cite/);
+});
+
+test('renders tab-separated summary tables and removes trailing emphasis junk', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const markdownIt = new MarkdownIt({ html: false, linkify: true, typographer: true, breaks: true });
+  const input = 'Summary Table\nSituation\tImaging Recommended\tTiming/Notes\nFirst febrile UTI\tRenal/bladder ultrasound\tAfter recovery\nRoutine use of DMSA scan\tNot recommended\t\n**';
+  const html = renderAssistantMarkdown(input, sources, { markdownIt });
+  assert.match(html, /<table>/);
+  assert.match(html, /<th>Situation<\/th>/);
+  assert.match(html, /<td>Routine use of DMSA scan<\/td>/);
+  assert.doesNotMatch(html, /\*\*/);
+});
+
+test('repairs split tab-separated clinical summary rows', async () => {
+  const { renderAssistantMarkdown } = await loadCitationModule();
+  const markdownIt = new MarkdownIt({ html: false, linkify: true, typographer: true, breaks: true });
+  const input = 'Summary Table\nStep\tDetails\tSource\nRed Flags\tShock, peritonitis, distension\t3 4 7\nInitial Imaging\tAbdominal X-ray if perforation suspected, then ultrasound\n2 3 7\t\tDiagnostic Gold Std\nAbdominal ultrasound target sign\t2 3 7 Nonoperative Reduction\tAir or contrast enema if stable\nSurgical Indications\tShock, peritonitis, perforation, failed reduction\n1 3 7\t\tRecurrence Rate\n~10% after nonsurgical reduction\t5 6 7\tIf you need details on recurrence management, please specify.';
+  const html = renderAssistantMarkdown(input, sources, { markdownIt, citationLabel: 'number' });
+  assert.match(html, /<table>/);
+  assert.match(html, /<td>Initial Imaging<\/td>/);
+  assert.match(html, /<td>Diagnostic Gold Std<\/td>/);
+  assert.match(html, /<td>Recurrence Rate<\/td>/);
+  assert.doesNotMatch(html, /If you need details/);
+});