feat(dna): Add CodeDNA extractor for codebase pattern analysis

.gitignore

@@ -34,3 +34,7 @@ backend/repos/
 # MCP Server
 mcp-server/__pycache__/
 *.code-workspace
+
+# Validation experiments
+validation-experiment/
+exp-2/

backend/dependencies.py

@@ -14,6 +14,7 @@
 from services.dependency_analyzer import DependencyAnalyzer
 from services.style_analyzer import StyleAnalyzer
 from services.performance_metrics import PerformanceMetrics
+from services.dna_extractor import DNAExtractor
 from services.rate_limiter import RateLimiter, APIKeyManager
 from services.supabase_service import get_supabase_service
 from services.input_validator import InputValidator, CostController
@@ -26,6 +27,7 @@
 repo_manager = RepositoryManager()
 dependency_analyzer = DependencyAnalyzer()
 style_analyzer = StyleAnalyzer()
+dna_extractor = DNAExtractor()
 metrics = PerformanceMetrics()
 
 # Rate limiting and API key management

backend/routes/analysis.py

@@ -3,7 +3,7 @@
 from pydantic import BaseModel
 
 from dependencies import (
-    dependency_analyzer, style_analyzer,
+    dependency_analyzer, style_analyzer, dna_extractor,
     get_repo_or_404
 )
 from services.input_validator import InputValidator
@@ -133,3 +133,50 @@ async def get_style_analysis(
         return {**style_data, "cached": False}
     except Exception as e:
         raise HTTPException(status_code=500, detail=str(e))
+
+
+
+@router.get("/{repo_id}/dna")
+async def get_codebase_dna(
+    repo_id: str,
+    format: str = "json",
+    auth: AuthContext = Depends(require_auth)
+):
+    """
+    Extract codebase DNA - architectural patterns, conventions, and constraints.
+
+    This endpoint analyzes your codebase and returns a DNA profile that helps
+    AI assistants understand how to write code consistent with your patterns.
+
+    Args:
+        repo_id: Repository identifier
+        format: Output format - 'json' or 'markdown' (default: json)
+
+    Returns:
+        DNA profile with auth patterns, service patterns, database patterns, etc.
+    """
+    try:
+        repo = get_repo_or_404(repo_id, auth.user_id)
+
+        # Try cache first
+        cached_dna = dna_extractor.load_from_cache(repo_id)
+        if cached_dna:
+            logger.debug("Using cached DNA", repo_id=repo_id)
+            if format == "markdown":
+                return {"dna": cached_dna.to_markdown(), "cached": True}
+            return {**cached_dna.to_dict(), "cached": True}
+
+        # Extract fresh DNA
+        logger.info("Extracting codebase DNA", repo_id=repo_id)
+        metrics.increment("dna_extractions")
+
+        dna = dna_extractor.extract_dna(repo["local_path"], repo_id)
+        dna_extractor.save_to_cache(repo_id, dna)
+
+        if format == "markdown":
+            return {"dna": dna.to_markdown(), "cached": False}
+        return {**dna.to_dict(), "cached": False}
+
+    except Exception as e:
+        logger.error("Error extracting DNA", repo_id=repo_id, error=str(e))
+        raise HTTPException(status_code=500, detail=str(e))