feat: implement compact chat references with numbered citations (#220)

Transform verbose inline references to compact footnote-style format:
- Replace [source:abc123] with numbered citations [1], [2], etc.
- Add "References:" section at bottom of messages
- Deduplicate references (same ID gets same number)
- Remove icons from citations for cleaner appearance
- Maintain click-to-open functionality for all reference types

Changes:
- Add convertReferencesToCompactMarkdown() function
- Add createCompactReferenceLinkComponent() function
- Update ChatPanel to use new compact reference functions
- Add ReferenceData interface for type safety

Improves readability by reducing visual clutter while preserving
all existing functionality. References restart numbering at 1 for
each message.

frontend/src/app/(dashboard)/notebooks/components/NotesColumn.tsx

@@ -105,7 +105,7 @@ export function NotesColumn({
                       ) : (
                         <User className="h-4 w-4 text-muted-foreground" />
                       )}
-                      <Badge variant={note.note_type === 'ai' ? 'default' : 'secondary'} className="text-xs">
+                      <Badge variant="secondary" className="text-xs">
                         {note.note_type === 'ai' ? 'AI Generated' : 'Human'}
                       </Badge>
                     </div>

frontend/src/components/source/ChatPanel.tsx

@@ -18,7 +18,7 @@ import { ModelSelector } from './ModelSelector'
 import { ContextIndicator } from '@/components/common/ContextIndicator'
 import { SessionManager } from '@/components/source/SessionManager'
 import { MessageActions } from '@/components/source/MessageActions'
-import { convertReferencesToMarkdownLinks, createReferenceLinkComponent } from '@/lib/utils/source-references'
+import { convertReferencesToCompactMarkdown, createCompactReferenceLinkComponent } from '@/lib/utils/source-references'
 import { useModalManager } from '@/lib/hooks/use-modal-manager'
 import { toast } from 'sonner'
 
@@ -326,11 +326,11 @@ function AIMessageContent({
   content: string
   onReferenceClick: (type: string, id: string) => void
 }) {
-  // Convert references to markdown links
-  const markdownWithLinks = convertReferencesToMarkdownLinks(content)
+  // Convert references to compact markdown with numbered citations
+  const markdownWithCompactRefs = convertReferencesToCompactMarkdown(content)
 
-  // Create custom link component
-  const LinkComponent = createReferenceLinkComponent(onReferenceClick)
+  // Create custom link component for compact references
+  const LinkComponent = createCompactReferenceLinkComponent(onReferenceClick)
 
   return (
     <div className="prose prose-sm prose-neutral dark:prose-invert max-w-none break-words prose-headings:font-semibold prose-a:text-blue-600 prose-a:break-all prose-code:bg-muted prose-code:px-1 prose-code:py-0.5 prose-code:rounded prose-p:mb-4 prose-p:leading-7 prose-li:mb-2">
@@ -349,7 +349,7 @@ function AIMessageContent({
           ol: ({ children }) => <ol className="mb-4 space-y-1">{children}</ol>,
         }}
       >
-        {markdownWithLinks}
+        {markdownWithCompactRefs}
       </ReactMarkdown>
     </div>
   )

frontend/src/lib/utils/source-references.tsx

@@ -23,6 +23,12 @@ export interface ExtractedReferences {
   references: ExtractedReference[]
 }
 
+export interface ReferenceData {
+  number: number
+  type: ReferenceType
+  id: string
+}
+
 /**
  * Parse source references from text
  *
@@ -307,6 +313,163 @@ export function createReferenceLinkComponent(
   return ReferenceLinkComponent
 }
 
+/**
+ * Convert references in text to compact numbered format with reference list
+ *
+ * This function transforms verbose inline references like [source:abc123] into
+ * compact numbered citations [1], [2], etc., and appends a "References:" section
+ * at the bottom of the message with the full reference details.
+ *
+ * Algorithm:
+ * 1. Parse all references using parseSourceReferences()
+ * 2. Build a reference map to deduplicate and assign numbers
+ * 3. Replace inline references with numbered citations
+ * 4. Append reference list at the bottom
+ *
+ * @param text - Original text with references
+ * @returns Text with numbered citations and reference list appended
+ *
+ * @example
+ * Input: "See [source:abc] and [note:xyz]. Also [source:abc] again."
+ * Output: "See [1] and [2]. Also [1] again.\n\nReferences:\n[1] - [source:abc]\n[2] - [note:xyz]"
+ */
+export function convertReferencesToCompactMarkdown(text: string): string {
+  // Step 1: Parse all references using existing function
+  const references = parseSourceReferences(text)
+
+  // Step 2: If no references found, return original text
+  if (references.length === 0) {
+    return text
+  }
+
+  // Step 3: Build reference map (deduplicate and assign numbers)
+  const referenceMap = new Map<string, ReferenceData>()
+  let nextNumber = 1
+
+  for (const reference of references) {
+    const key = `${reference.type}:${reference.id}`
+    if (!referenceMap.has(key)) {
+      referenceMap.set(key, {
+        number: nextNumber++,
+        type: reference.type,
+        id: reference.id
+      })
+    }
+  }
+
+  // Step 4: Replace references with numbered citations (process from end to start)
+  let result = text
+  for (let i = references.length - 1; i >= 0; i--) {
+    const reference = references[i]
+    const key = `${reference.type}:${reference.id}`
+    const refData = referenceMap.get(key)!
+    const number = refData.number
+
+    // Analyze context around the reference
+    const refStart = reference.startIndex
+    const refEnd = reference.endIndex
+    const contextBefore = result.substring(Math.max(0, refStart - 2), refStart)
+    const contextAfter = result.substring(refEnd, Math.min(result.length, refEnd + 2))
+
+    // Determine what to replace based on bracket context
+    let replaceStart = refStart
+    let replaceEnd = refEnd
+
+    // Check for double brackets [[ref]]
+    if (contextBefore === '[[' && contextAfter.startsWith(']]')) {
+      replaceStart = refStart - 2
+      replaceEnd = refEnd + 2
+    }
+    // Check for single brackets [ref]
+    else if (contextBefore.endsWith('[') && contextAfter.startsWith(']')) {
+      replaceStart = refStart - 1
+      replaceEnd = refEnd + 1
+    }
+
+    // Build the numbered citation with full reference in href
+    const citationLink = `[${number}](#ref-${reference.type}-${reference.id})`
+
+    // Replace in the result string
+    result = result.substring(0, replaceStart) + citationLink + result.substring(replaceEnd)
+  }
+
+  // Step 5: Build reference list
+  const refListLines: string[] = ['\n\nReferences:']
+
+  // Iterate through reference map in insertion order (Map preserves order)
+  for (const [, refData] of referenceMap) {
+    const refListItem = `[${refData.number}] - [${refData.type}:${refData.id}](#ref-${refData.type}-${refData.id})`
+    refListLines.push(refListItem)
+  }
+
+  // Step 6: Append reference list to result
+  result = result + refListLines.join('\n')
+
+  return result
+}
+
+/**
+ * Create a custom link component for ReactMarkdown that handles compact reference links
+ *
+ * This component handles two types of reference links:
+ * 1. Numbered citations in text: [1](#ref-source-abc123)
+ * 2. Reference list items: [source:abc123](#ref-source-abc123)
+ *
+ * Both use the same href format: #ref-{type}-{id}
+ * The component extracts the type and id from the href and triggers the click handler.
+ *
+ * @param onReferenceClick - Callback for when a reference link is clicked
+ * @returns React component for rendering links in ReactMarkdown
+ *
+ * @example
+ * const LinkComponent = createCompactReferenceLinkComponent((type, id) => openModal(type, id))
+ * <ReactMarkdown components={{ a: LinkComponent }}>...</ReactMarkdown>
+ */
+export function createCompactReferenceLinkComponent(
+  onReferenceClick: (type: ReferenceType, id: string) => void
+) {
+  const CompactReferenceLinkComponent = ({
+    href,
+    children,
+    ...props
+  }: React.AnchorHTMLAttributes<HTMLAnchorElement> & {
+    href?: string
+    children?: React.ReactNode
+  }) => {
+    // Check if this is a reference link (starts with #ref-)
+    if (href?.startsWith('#ref-')) {
+      // Parse: #ref-source-abc123 → type=source, id=abc123
+      const parts = href.substring(5).split('-') // Remove '#ref-'
+      const type = parts[0] as ReferenceType
+      const id = parts.slice(1).join('-') // Rejoin in case ID has dashes
+
+      return (
+        <button
+          onClick={(e) => {
+            e.preventDefault()
+            e.stopPropagation()
+            onReferenceClick(type, id)
+          }}
+          className="text-primary hover:underline cursor-pointer inline font-medium"
+          type="button"
+        >
+          {children}
+        </button>
+      )
+    }
+
+    // Regular link - open in new tab
+    return (
+      <a href={href} target="_blank" rel="noopener noreferrer" {...props} className="text-primary hover:underline">
+        {children}
+      </a>
+    )
+  }
+
+  CompactReferenceLinkComponent.displayName = 'CompactReferenceLinkComponent'
+  return CompactReferenceLinkComponent
+}
+
 /**
  * Legacy function for backward compatibility
  * Converts old Link-based references to new click handler approach