feat: add MCP server and legacy code for reference

MCP Server:
- Standalone Model Context Protocol server implementation
- Enables Claude/AI agents to interact with CodeIntel
- Python-based server with websocket support
- Configuration via environment variables
- Can run independently or alongside main backend

Legacy Code:
- Previous iteration implementations preserved for reference
- Old indexer and repo manager versions
- React component examples
- Useful for understanding evolution of the codebase
- Marked as legacy to avoid confusion with current implementation

Note: MCP server is optional and not required for main application

Author: DevanshuNEU

legacy/IndexingProgress.tsx

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+import { useEffect, useState } from 'react'
+
+interface IndexingProgressProps {
+  repoId: string
+  apiUrl: string
+  apiKey: string
+  onComplete: () => void
+}
+
+export function IndexingProgress({ repoId, apiUrl, apiKey, onComplete }: IndexingProgressProps) {
+  const [progress, setProgress] = useState(0)
+  const [status, setStatus] = useState('Starting...')
+  const [stats, setStats] = useState({ processed: 0, total: 0, functions: 0 })
+
+  useEffect(() => {
+    let interval: any
+    
+    const checkProgress = async () => {
+      try {
+        const response = await fetch(`${apiUrl}/api/repos/${repoId}`, {
+          headers: { 'Authorization': `Bearer ${apiKey}` }
+        })
+        const repo = await response.json()
+        
+        if (repo.status === 'indexed') {
+          setProgress(100)
+          setStatus('✅ Indexing complete!')
+          clearInterval(interval)
+          setTimeout(onComplete, 1500)
+        } else if (repo.status === 'indexing') {
+          // Estimate progress based on function count growth
+          const estimatedProgress = Math.min(95, (repo.file_count / 100) * 100)
+          setProgress(estimatedProgress)
+          setStatus(`📊 Indexing... ${repo.file_count} functions processed`)
+          setStats({
+            processed: repo.file_count,
+            total: 100,
+            functions: repo.file_count
+          })
+        }
+      } catch (error) {
+        console.error('Error checking progress:', error)
+      }
+    }
+    
+    // Check immediately, then every 2 seconds
+    checkProgress()
+    interval = setInterval(checkProgress, 2000)
+    
+    return () => clearInterval(interval)
+  }, [repoId])
+
+  return (
+    <div className="fixed inset-0 bg-black/50 flex items-center justify-center z-50">
+      <div className="bg-white rounded-lg shadow-xl p-8 max-w-md w-full mx-4">
+        <h3 className="text-xl font-semibold mb-6 text-gray-900">
+          Indexing Repository
+        </h3>
+        
+        <div className="space-y-4">
+          <div className="flex items-center justify-between text-sm mb-2">
+            <span className="text-gray-600">{status}</span>
+            <span className="font-semibold text-blue-600">{progress.toFixed(0)}%</span>
+          </div>
+          
+          {/* Progress Bar */}
+          <div className="w-full bg-gray-200 rounded-full h-3 overflow-hidden">
+            <div 
+              className="h-full bg-gradient-to-r from-blue-500 to-blue-600 transition-all duration-500 ease-out"
+              style={{ width: `${progress}%` }}
+            />
+          </div>
+          
+          {/* Stats */}
+          {stats.functions > 0 && (
+            <div className="grid grid-cols-2 gap-3 mt-4 pt-4 border-t border-gray-200">
+              <div>
+                <div className="text-xs text-gray-500">Functions Found</div>
+                <div className="text-2xl font-bold text-gray-900">{stats.functions}</div>
+              </div>
+              <div>
+                <div className="text-xs text-gray-500">Status</div>
+                <div className="text-sm font-semibold text-blue-600">Processing...</div>
+              </div>
+            </div>
+          )}
+          
+          <p className="text-xs text-gray-500 mt-4">
+            Using batch processing for optimal performance
+          </p>
+        </div>
+      </div>
+    </div>
+  )
+}

legacy/README.md

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+# Legacy Code Archive
+
+This folder contains old implementations that were replaced during development.
+
+## Files:
+
+### indexer_old.py
+- Original indexer implementation before batch processing optimization
+- Replaced by `indexer_optimized.py` which achieves 100x performance improvement
+- Kept for reference on the evolution from individual API calls to batch processing
+
+### repo_manager_old.py  
+- Original repository manager with in-memory storage
+- Replaced by current `repo_manager.py` with Supabase persistence
+- Shows the migration from ephemeral to production-grade storage
+
+### IndexingProgress.tsx
+- Original indexing progress component using WebSocket
+- Replaced by integrated progress in `RepoOverview.tsx` using shadcn Progress component
+- Kept for reference on the WebSocket implementation approach
+
+**Note:** These files are not imported or used anywhere in the active codebase.
+They're preserved for historical reference and to show the development evolution.