fix response formatting

phd-advisor-frontend/package-lock.json

@@ -15,6 +15,7 @@
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         "react": "^19.1.0",
         "react-dom": "^19.1.0",
+        "react-markdown": "^10.1.0",
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         "web-vitals": "^2.1.4"
       }
@@ -3640,6 +3641,15 @@
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+      "license": "MIT",
+      "dependencies": {
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+    "node_modules/@types/estree-jsx": {
+      "version": "1.0.5",
+      "resolved": "https://registry.npmjs.org/@types/estree-jsx/-/estree-jsx-1.0.5.tgz",
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+      "license": "MIT",
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@@ -3711,6 +3730,15 @@
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       }
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+      "resolved": "https://registry.npmjs.org/@types/hast/-/hast-3.0.4.tgz",
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+      "license": "MIT",
+      "dependencies": {
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+      }
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+      "license": "MIT",
+      "dependencies": {
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+      }
+    },
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+    "node_modules/@types/ms": {
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+      "resolved": "https://registry.npmjs.org/@types/ms/-/ms-2.1.0.tgz",
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+      "license": "MIT"
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@@ -3822,6 +3865,16 @@
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+    "node_modules/@types/react": {
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+      "resolved": "https://registry.npmjs.org/@types/react/-/react-19.1.9.tgz",
+      "integrity": "sha512-WmdoynAX8Stew/36uTSVMcLJJ1KRh6L3IZRx1PZ7qJtBqT3dYTgyDTx8H1qoRghErydW7xw9mSJ3wS//tCRpFA==",
+      "license": "MIT",
+      "peer": true,
+      "dependencies": {
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+      }
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@@ -3894,6 +3947,12 @@
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+    "node_modules/@types/unist": {
+      "version": "3.0.3",
+      "resolved": "https://registry.npmjs.org/@types/unist/-/unist-3.0.3.tgz",
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@@ -5151,6 +5210,16 @@
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+      "resolved": "https://registry.npmjs.org/bail/-/bail-2.0.2.tgz",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
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@@ -5497,6 +5566,16 @@
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     },
+    "node_modules/ccount": {
+      "version": "2.0.1",
+      "resolved": "https://registry.npmjs.org/ccount/-/ccount-2.0.1.tgz",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
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@@ -5522,6 +5601,46 @@
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       }
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+      "resolved": "https://registry.npmjs.org/character-entities/-/character-entities-2.0.2.tgz",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
+    },
+    "node_modules/character-entities-html4": {
+      "version": "2.1.0",
+      "resolved": "https://registry.npmjs.org/character-entities-html4/-/character-entities-html4-2.1.0.tgz",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
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+    "node_modules/character-entities-legacy": {
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+      "resolved": "https://registry.npmjs.org/character-entities-legacy/-/character-entities-legacy-3.0.0.tgz",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
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+    "node_modules/character-reference-invalid": {
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
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@@ -5769,6 +5888,16 @@
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+    "node_modules/comma-separated-tokens": {
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
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+      "funding": {
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+      "funding": {
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+        "url": "https://github.com/sponsors/wooorm"
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@@ -7773,6 +7935,16 @@
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+    "node_modules/estree-util-is-identifier-name": {
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+      "resolved": "https://registry.npmjs.org/estree-util-is-identifier-name/-/estree-util-is-identifier-name-3.0.0.tgz",
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+      "funding": {
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@@ -8838,6 +9016,46 @@
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+    "node_modules/hast-util-to-jsx-runtime": {
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+      "dependencies": {
+        "@types/estree": "^1.0.0",
+        "@types/hast": "^3.0.0",
+        "@types/unist": "^3.0.0",
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+        "devlop": "^1.0.0",
+        "estree-util-is-identifier-name": "^3.0.0",
+        "hast-util-whitespace": "^3.0.0",
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+        "mdast-util-mdx-jsx": "^3.0.0",
+        "mdast-util-mdxjs-esm": "^2.0.0",
+        "property-information": "^7.0.0",
+        "space-separated-tokens": "^2.0.0",
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+        "unist-util-position": "^5.0.0",
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+        "url": "https://opencollective.com/unified"
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+    "node_modules/hast-util-whitespace": {
+      "version": "3.0.0",
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+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
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+    "node_modules/is-alphanumerical": {
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+      "license": "MIT",
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@@ -9426,6 +9684,16 @@
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+      "license": "MIT",
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+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-position": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/unist-util-position/-/unist-util-position-5.0.0.tgz",
+      "integrity": "sha512-fucsC7HjXvkB5R3kTCO7kUjRdrS0BJt3M/FPxmHMBOm8JQi2BsHAHFsy27E0EolP8rp0NzXsJ+jNPyDWvOJZPA==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-stringify-position": {
+      "version": "4.0.0",
+      "resolved": "https://registry.npmjs.org/unist-util-stringify-position/-/unist-util-stringify-position-4.0.0.tgz",
+      "integrity": "sha512-0ASV06AAoKCDkS2+xw5RXJywruurpbC4JZSm7nr7MOt1ojAzvyyaO+UxZf18j8FCF6kmzCZKcAgN/yu2gm2XgQ==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-visit": {
+      "version": "5.0.0",
+      "resolved": "https://registry.npmjs.org/unist-util-visit/-/unist-util-visit-5.0.0.tgz",
+      "integrity": "sha512-MR04uvD+07cwl/yhVuVWAtw+3GOR/knlL55Nd/wAdblk27GCVt3lqpTivy/tkJcZoNPzTwS1Y+KMojlLDhoTzg==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-is": "^6.0.0",
+        "unist-util-visit-parents": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/unist-util-visit-parents": {
+      "version": "6.0.1",
+      "resolved": "https://registry.npmjs.org/unist-util-visit-parents/-/unist-util-visit-parents-6.0.1.tgz",
+      "integrity": "sha512-L/PqWzfTP9lzzEa6CKs0k2nARxTdZduw3zyh8d2NVBnsyvHjSX4TWse388YrrQKbvI8w20fGjGlhgT96WwKykw==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-is": "^6.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
     "node_modules/universalify": {
       "version": "2.0.1",
       "resolved": "https://registry.npmjs.org/universalify/-/universalify-2.0.1.tgz",
@@ -16623,6 +17762,34 @@
         "node": ">= 0.8"
       }
     },
+    "node_modules/vfile": {
+      "version": "6.0.3",
+      "resolved": "https://registry.npmjs.org/vfile/-/vfile-6.0.3.tgz",
+      "integrity": "sha512-KzIbH/9tXat2u30jf+smMwFCsno4wHVdNmzFyL+T/L3UGqqk6JKfVqOFOZEpZSHADH1k40ab6NUIXZq422ov3Q==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "vfile-message": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
+    "node_modules/vfile-message": {
+      "version": "4.0.3",
+      "resolved": "https://registry.npmjs.org/vfile-message/-/vfile-message-4.0.3.tgz",
+      "integrity": "sha512-QTHzsGd1EhbZs4AsQ20JX1rC3cOlt/IWJruk893DfLRr57lcnOeMaWG4K0JrRta4mIJZKth2Au3mM3u03/JWKw==",
+      "license": "MIT",
+      "dependencies": {
+        "@types/unist": "^3.0.0",
+        "unist-util-stringify-position": "^4.0.0"
+      },
+      "funding": {
+        "type": "opencollective",
+        "url": "https://opencollective.com/unified"
+      }
+    },
     "node_modules/w3c-hr-time": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/w3c-hr-time/-/w3c-hr-time-1.0.2.tgz",
@@ -17560,6 +18727,16 @@
       "funding": {
         "url": "https://github.com/sponsors/sindresorhus"
       }
+    },
+    "node_modules/zwitch": {
+      "version": "2.0.4",
+      "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz",
+      "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==",
+      "license": "MIT",
+      "funding": {
+        "type": "github",
+        "url": "https://github.com/sponsors/wooorm"
+      }
     }
   }
 }

phd-advisor-frontend/package.json

@@ -10,6 +10,7 @@
     "lucide-react": "^0.513.0",
     "react": "^19.1.0",
     "react-dom": "^19.1.0",
+    "react-markdown": "^10.1.0",
     "react-scripts": "5.0.1",
     "web-vitals": "^2.1.4"
   },

phd-advisor-frontend/src/components/AdvisorStatusDropdown.js

@@ -4,7 +4,18 @@ import { Users, ChevronDown } from 'lucide-react';
 const AdvisorStatusDropdown = ({ advisors, thinkingAdvisors, getAdvisorColors, isDark }) => {
   const [isOpen, setIsOpen] = useState(false);
   
-  // Safety checks
+  // Close dropdown when clicking outside
+  useEffect(() => {
+    const handleClickOutside = (event) => {
+      if (isOpen && !event.target.closest('.advisor-status-dropdown')) {
+        setIsOpen(false);
+      }
+    };
+
+    document.addEventListener('mousedown', handleClickOutside);
+    return () => document.removeEventListener('mousedown', handleClickOutside);
+  }, [isOpen]);
+
   if (!advisors || typeof advisors !== 'object') {
     return null;
   }
@@ -19,18 +30,6 @@ const AdvisorStatusDropdown = ({ advisors, thinkingAdvisors, getAdvisorColors, i
     setIsOpen(!isOpen);
   };
 
-  // Close dropdown when clicking outside
-  useEffect(() => {
-    const handleClickOutside = (event) => {
-      if (isOpen && !event.target.closest('.advisor-status-dropdown')) {
-        setIsOpen(false);
-      }
-    };
-
-    document.addEventListener('mousedown', handleClickOutside);
-    return () => document.removeEventListener('mousedown', handleClickOutside);
-  }, [isOpen]);
-
   return (
     <div className="advisor-status-dropdown">
       <button 

phd-advisor-frontend/src/components/MessageBubble.js

@@ -1,4 +1,5 @@
 import React, { useState, useRef, useEffect } from 'react';
+import ReactMarkdown from 'react-markdown';
 import { Reply, Copy, Check, Maximize2, Info, FileText, Hash, Target } from 'lucide-react';
 import { advisors, getAdvisorColors } from '../data/advisors';
 import { useTheme } from '../contexts/ThemeContext';
@@ -22,7 +23,6 @@ const MessageBubble = ({
       setCopiedStates(prev => ({ ...prev, [messageId]: true }));
       if (onCopy) onCopy(messageId, content);
       
-      // Reset the copied state after 2 seconds
       setTimeout(() => {
         setCopiedStates(prev => ({ ...prev, [messageId]: false }));
       }, 2000);
@@ -63,6 +63,172 @@ const MessageBubble = ({
     }
   }, [showInfoOverlay]);
 
+  // Preprocess markdown content to fix common formatting issues
+  const preprocessMarkdown = (content) => {
+    if (!content) return '';
+    
+    // Ensure proper line breaks before numbered lists
+    let processed = content.replace(/(\d+\.\s\*\*[^*]+\*\*)/g, '\n\n$1');
+    
+    // Ensure proper line breaks after list items
+    processed = processed.replace(/(\d+\.\s[^\n]+)(?=\s+\d+\.)/g, '$1\n');
+    
+    // Fix spacing around bold headers
+    processed = processed.replace(/(\*\*[^*]+\*\*)/g, '\n\n$1\n\n');
+    
+    // Clean up multiple consecutive line breaks
+    processed = processed.replace(/\n{3,}/g, '\n\n');
+    
+    // Ensure proper paragraph breaks
+    processed = processed.replace(/([.!?])\s+([A-Z])/g, '$1\n\n$2');
+    
+    return processed.trim();
+  };
+
+  // ENHANCED MARKDOWN COMPONENTS WITH BETTER STYLING
+  const markdownComponents = {
+    // Bold text styling - for headers and key terms
+    strong: ({ children }) => (
+      <strong style={{ 
+        fontWeight: '700',
+        color: isDark ? '#ffffff' : '#1f2937',
+        display: 'block',
+        marginBottom: '0.5rem',
+        marginTop: '1rem'
+      }}>
+        {children}
+      </strong>
+    ),
+    
+    // Italic text styling
+    em: ({ children }) => (
+      <em style={{ 
+        fontStyle: 'italic',
+        color: isDark ? '#93c5fd' : '#3b82f6',
+        fontWeight: '500'
+      }}>
+        {children}
+      </em>
+    ),
+    
+    // Paragraph styling with proper spacing
+    p: ({ children }) => (
+      <p style={{ 
+        marginBottom: '1rem',
+        lineHeight: '1.7',
+        color: isDark ? '#e5e7eb' : '#374151',
+        fontSize: '14px'
+      }}>
+        {children}
+      </p>
+    ),
+    
+    // Unordered list styling
+    ul: ({ children }) => (
+      <ul style={{ 
+        listStyleType: 'disc',
+        paddingLeft: '1.5rem',
+        marginBottom: '1rem',
+        marginTop: '0.5rem',
+        color: isDark ? '#e5e7eb' : '#374151'
+      }}>
+        {children}
+      </ul>
+    ),
+    
+    // Ordered list styling with better spacing
+    ol: ({ children }) => (
+      <ol style={{ 
+        listStyleType: 'decimal',
+        paddingLeft: '1.5rem',
+        marginBottom: '1rem',
+        marginTop: '0.5rem',
+        color: isDark ? '#e5e7eb' : '#374151',
+        counterReset: 'list-counter'
+      }}>
+        {children}
+      </ol>
+    ),
+    
+    // List item styling with proper spacing
+    li: ({ children }) => (
+      <li style={{ 
+        marginBottom: '0.75rem',
+        lineHeight: '1.6',
+        paddingLeft: '0.25rem'
+      }}>
+        {children}
+      </li>
+    ),
+
+    // Headers (in case they use them)
+    h1: ({ children }) => (
+      <h1 style={{
+        fontSize: '1.5rem',
+        fontWeight: '700',
+        color: isDark ? '#ffffff' : '#1f2937',
+        marginBottom: '1rem',
+        marginTop: '1.5rem',
+        borderBottom: `2px solid ${isDark ? '#374151' : '#e5e7eb'}`,
+        paddingBottom: '0.5rem'
+      }}>
+        {children}
+      </h1>
+    ),
+
+    h2: ({ children }) => (
+      <h2 style={{
+        fontSize: '1.25rem',
+        fontWeight: '600',
+        color: isDark ? '#ffffff' : '#1f2937',
+        marginBottom: '0.75rem',
+        marginTop: '1.25rem'
+      }}>
+        {children}
+      </h2>
+    ),
+
+    h3: ({ children }) => (
+      <h3 style={{
+        fontSize: '1.125rem',
+        fontWeight: '600',
+        color: isDark ? '#ffffff' : '#1f2937',
+        marginBottom: '0.5rem',
+        marginTop: '1rem'
+      }}>
+        {children}
+      </h3>
+    ),
+
+    // Code styling
+    code: ({ children }) => (
+      <code style={{ 
+        backgroundColor: isDark ? '#374151' : '#f3f4f6',
+        padding: '0.125rem 0.375rem',
+        borderRadius: '0.25rem',
+        fontSize: '0.875rem',
+        fontFamily: 'ui-monospace, SFMono-Regular, Consolas, monospace',
+        color: isDark ? '#fbbf24' : '#d97706'
+      }}>
+        {children}
+      </code>
+    ),
+
+    // Block quote styling
+    blockquote: ({ children }) => (
+      <blockquote style={{
+        borderLeft: '4px solid ' + (isDark ? '#374151' : '#e5e7eb'),
+        paddingLeft: '1rem',
+        marginLeft: '0',
+        marginBottom: '1rem',
+        fontStyle: 'italic',
+        color: isDark ? '#9ca3af' : '#6b7280'
+      }}>
+        {children}
+      </blockquote>
+    )
+  };
+
   // RAG Metadata Component
   const RagInfoOverlay = ({ ragMetadata, colors }) => {
     const hasDocuments = ragMetadata?.usedDocuments || false;
@@ -84,7 +250,6 @@ const MessageBubble = ({
         </div>
         
         <div className="rag-overlay-content">
-          {/* Basic Stats */}
           <div className="rag-stat-row">
             <div className="rag-stat-label">Used Documents:</div>
             <div className={`rag-stat-value ${hasDocuments ? 'positive' : 'negative'}`}>
@@ -97,7 +262,6 @@ const MessageBubble = ({
             <div className="rag-stat-value">{chunksUsed}</div>
           </div>
 
-          {/* Document Details */}
           {hasDocuments && documentChunks.length > 0 && (
             <div className="rag-documents-section">
               <div className="rag-section-title">
@@ -128,7 +292,6 @@ const MessageBubble = ({
             </div>
           )}
 
-          {/* No Documents Message */}
           {!hasDocuments && (
             <div className="rag-no-documents">
               <Hash size={12} />
@@ -175,7 +338,7 @@ const MessageBubble = ({
           style={{ 
             backgroundColor: colors.bgColor,
             borderColor: colors.color + '40',
-            position: 'relative' // For overlay positioning
+            position: 'relative'
           }}
         >
           <div className="advisor-message-header">
@@ -200,18 +363,27 @@ const MessageBubble = ({
               })}
             </span>
           </div>
-          <p 
+          
+          {/* Enhanced markdown rendering with preprocessing */}
+          <div 
             className="advisor-message-text"
             style={{ 
               color: colors.textColor
             }}
           >
-            {message.content}
-          </p>
+            <ReactMarkdown 
+              components={markdownComponents}
+              // Add these props for better parsing
+              remarkPlugins={[]}
+              rehypePlugins={[]}
+            >
+              {preprocessMarkdown(message.content)}
+            </ReactMarkdown>
+          </div>
+          
           {showReplyButton && (
             <div className="message-actions">
               <div className="action-buttons">
-                {/* Reply Button */}
                 <div className="tooltip-container">
                   <button 
                     className="action-button"
@@ -230,7 +402,6 @@ const MessageBubble = ({
                   )}
                 </div>
 
-                {/* Copy Button */}
                 <div className="tooltip-container">
                   <button 
                     className="action-button"
@@ -251,7 +422,6 @@ const MessageBubble = ({
                   )}
                 </div>
 
-                {/* Expand/Elaborate Button */}
                 <div className="tooltip-container">
                   <button 
                     className="action-button"
@@ -273,7 +443,6 @@ const MessageBubble = ({
             </div>
           )}
 
-          {/* RAG Info Overlay */}
           {showInfoOverlay && (
             <RagInfoOverlay 
               ragMetadata={message.ragMetadata} 

phd-advisor-frontend/src/styles/components.css

@@ -551,9 +551,39 @@
 
 .advisor-message-text {
   line-height: 1.6;
-  margin: 0;
 }
 
+.advisor-message-text > div:last-child p:last-child {
+  margin-bottom: 0; /* Remove bottom margin from last paragraph */
+}
+
+.advisor-message-text strong {
+  font-weight: 600;
+}
+
+.advisor-message-text em {
+  font-style: italic;
+}
+
+.advisor-message-text ul,
+.advisor-message-text ol {
+  margin: 0.75rem 0;
+  padding-left: 1.5rem;
+}
+
+.advisor-message-text li {
+  margin-bottom: 0.25rem;
+}
+
+.advisor-message-text p {
+  margin-bottom: 0.75rem;
+}
+
+.advisor-message-text p:last-child {
+  margin-bottom: 0;
+}
+
+
 /* Updated Message Actions Styles */
 .message-actions {
   margin-top: 12px;
@@ -1100,6 +1130,10 @@
     font-size: 13px;
   }
 
+  .advisor-message-text {
+    font-size: 14px;
+  }
+
   /* Basic ChatInput mobile styles */
   .input-container .send-text {
     display: inline;