feat(dashboard): Enhanced chat, spec management, and Claude integration

Backend:
- spec.py: New AtomizerSpec REST API endpoints
- spec_manager.py: SpecManager service for unified config
- interview_engine.py: Study creation interview logic
- claude.py: Enhanced Claude API with context
- optimization.py: Extended optimization endpoints
- context_builder.py, session_manager.py: Improved services

Frontend:
- Chat components: Enhanced message rendering, tool call cards
- Hooks: useClaudeCode, useSpecWebSocket, improved useChat
- Pages: Updated Dashboard, Analysis, Insights, Setup, Home
- Components: ParallelCoordinatesPlot, ParetoPlot improvements
- App.tsx: Route updates for canvas/studio

Infrastructure:
- vite.config.ts: Build configuration updates
- start/stop-dashboard.bat: Script improvements

atomizer-dashboard/backend/api/services/session_manager.py

@@ -219,6 +219,18 @@ class SessionManager:
                 full_response = result["stdout"] or ""
 
                 if full_response:
+                    # Check if response contains canvas modifications (from MCP tools)
+                    import logging
+                    logger = logging.getLogger(__name__)
+
+                    modifications = self._extract_canvas_modifications(full_response)
+                    logger.info(f"[SEND_MSG] Found {len(modifications)} canvas modifications to send")
+
+                    for mod in modifications:
+                        logger.info(f"[SEND_MSG] Sending canvas_modification: {mod.get('action')} {mod.get('nodeType')}")
+                        yield {"type": "canvas_modification", "modification": mod}
+
+                    # Always send the text response
                     yield {"type": "text", "content": full_response}
 
                 if result["returncode"] != 0 and result["stderr"]:
@@ -292,6 +304,90 @@ class SessionManager:
             **({} if not db_record else {"db_record": db_record}),
         }
 
+    def _extract_canvas_modifications(self, response: str) -> List[Dict]:
+        """
+        Extract canvas modification objects from Claude's response.
+
+        MCP tools like canvas_add_node return JSON with a 'modification' field.
+        This method finds and extracts those modifications so the frontend can apply them.
+        """
+        import re
+        import logging
+        logger = logging.getLogger(__name__)
+
+        modifications = []
+
+        # Debug: log what we're searching
+        logger.info(f"[CANVAS_MOD] Searching response ({len(response)} chars) for modifications")
+
+        # Check if "modification" even exists in the response
+        if '"modification"' not in response:
+            logger.info("[CANVAS_MOD] No 'modification' key found in response")
+            return modifications
+
+        try:
+            # Method 1: Look for JSON in code fences
+            code_block_pattern = r'```(?:json)?\s*([\s\S]*?)```'
+            for match in re.finditer(code_block_pattern, response):
+                block_content = match.group(1).strip()
+                try:
+                    obj = json.loads(block_content)
+                    if isinstance(obj, dict) and 'modification' in obj:
+                        logger.info(f"[CANVAS_MOD] Found modification in code fence: {obj['modification']}")
+                        modifications.append(obj['modification'])
+                except json.JSONDecodeError:
+                    continue
+
+            # Method 2: Find JSON objects using proper brace matching
+            # This handles nested objects correctly
+            i = 0
+            while i < len(response):
+                if response[i] == '{':
+                    # Found a potential JSON start, find matching close
+                    brace_count = 1
+                    j = i + 1
+                    in_string = False
+                    escape_next = False
+
+                    while j < len(response) and brace_count > 0:
+                        char = response[j]
+
+                        if escape_next:
+                            escape_next = False
+                        elif char == '\\':
+                            escape_next = True
+                        elif char == '"' and not escape_next:
+                            in_string = not in_string
+                        elif not in_string:
+                            if char == '{':
+                                brace_count += 1
+                            elif char == '}':
+                                brace_count -= 1
+                        j += 1
+
+                    if brace_count == 0:
+                        potential_json = response[i:j]
+                        try:
+                            obj = json.loads(potential_json)
+                            if isinstance(obj, dict) and 'modification' in obj:
+                                mod = obj['modification']
+                                # Avoid duplicates
+                                if mod not in modifications:
+                                    logger.info(f"[CANVAS_MOD] Found inline modification: action={mod.get('action')}, nodeType={mod.get('nodeType')}")
+                                    modifications.append(mod)
+                        except json.JSONDecodeError as e:
+                            # Not valid JSON, skip
+                            pass
+                    i = j
+                else:
+                    i += 1
+
+        except Exception as e:
+            logger.error(f"[CANVAS_MOD] Error extracting modifications: {e}")
+
+        logger.info(f"[CANVAS_MOD] Extracted {len(modifications)} modification(s)")
+        return modifications
+
     def _build_mcp_config(self, mode: Literal["user", "power"]) -> dict:
         """Build MCP configuration for Claude"""
         return {