feat: Add dashboard chat integration and MCP server

Major changes:
- Dashboard: WebSocket-based chat with session management
- Dashboard: New chat components (ChatPane, ChatInput, ModeToggle)
- Dashboard: Enhanced UI with parallel coordinates chart
- MCP Server: New atomizer-tools server for Claude integration
- Extractors: Enhanced Zernike OPD extractor
- Reports: Improved report generator

New studies (configs and scripts only):
- M1 Mirror: Cost reduction campaign studies
- Simple Beam, Simple Bracket, UAV Arm studies

Note: Large iteration data (2_iterations/, best_design_archive/)
excluded via .gitignore - kept on local Gitea only.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

mcp-server/atomizer-tools/src/utils/paths.ts

@@ -0,0 +1,50 @@
+/**
+ * Path utilities for Atomizer MCP server
+ */
+
+import { fileURLToPath } from 'url';
+import { dirname, resolve } from 'path';
+
+// Get directory of current file
+const __filename = fileURLToPath(import.meta.url);
+const __dirname = dirname(__filename);
+
+// Atomizer root directory
+export const ATOMIZER_ROOT = resolve(__dirname, '../../../../..');
+
+// Key directories
+export const STUDIES_DIR = resolve(ATOMIZER_ROOT, 'studies');
+export const OPTIMIZATION_ENGINE_DIR = resolve(ATOMIZER_ROOT, 'optimization_engine');
+export const DOCS_DIR = resolve(ATOMIZER_ROOT, 'docs');
+
+// Python configuration
+export const PYTHON_PATH = process.env.ATOMIZER_PYTHON_PATH ||
+  'C:/Users/antoi/anaconda3/envs/atomizer/python.exe';
+
+// Mode from environment
+export const ATOMIZER_MODE = (process.env.ATOMIZER_MODE || 'user') as 'user' | 'power';
+
+// Check if a path is within Atomizer root (security)
+export function isPathAllowed(path: string): boolean {
+  const resolved = resolve(path);
+  return resolved.startsWith(ATOMIZER_ROOT);
+}
+
+// Get study directory
+export function getStudyDir(studyName: string): string {
+  return resolve(STUDIES_DIR, studyName);
+}
+
+// Get study database path
+export function getStudyDbPath(studyName: string): string {
+  return resolve(getStudyDir(studyName), '3_results', 'study.db');
+}
+
+// Get study config path
+export function getStudyConfigPath(studyName: string): string {
+  const setupConfig = resolve(getStudyDir(studyName), '1_setup', 'optimization_config.json');
+  const rootConfig = resolve(getStudyDir(studyName), 'optimization_config.json');
+
+  // Check which exists - prefer 1_setup/
+  return setupConfig; // Let caller handle if it doesn't exist
+}