feat: Add Studio UI, intake system, and extractor improvements

Dashboard:
- Add Studio page with drag-drop model upload and Claude chat
- Add intake system for study creation workflow
- Improve session manager and context builder
- Add intake API routes and frontend components

Optimization Engine:
- Add CLI module for command-line operations
- Add intake module for study preprocessing
- Add validation module with gate checks
- Improve Zernike extractor documentation
- Update spec models with better validation
- Enhance solve_simulation robustness

Documentation:
- Add ATOMIZER_STUDIO.md planning doc
- Add ATOMIZER_UX_SYSTEM.md for UX patterns
- Update extractor library docs
- Add study-readme-generator skill

Tools:
- Add test scripts for extraction validation
- Add Zernike recentering test

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

studies/M1_Mirror/m1_mirror_cost_reduction_lateral/3_results/optimization_summary.json

@@ -4,7 +4,7 @@
   "extraction_method": "ZernikeOPD_Annular",
   "inner_radius_mm": 135.75,
   "objectives_note": "Mass NOT in objective - WFE only",
-  "total_trials": 169,
+  "total_trials": 171,
   "feasible_trials": 167,
   "best_trial": {
     "number": 163,
@@ -24,5 +24,5 @@
     },
     "iter_folder": "C:\\Users\\antoi\\Atomizer\\studies\\M1_Mirror\\m1_mirror_cost_reduction_lateral\\2_iterations\\iter164"
   },
-  "timestamp": "2026-01-14T17:59:38.649254"
+  "timestamp": "2026-01-20T16:12:29.817282"
 }

studies/M1_Mirror/m1_mirror_cost_reduction_lateral/atomizer_spec.json

@@ -2,9 +2,9 @@
   "meta": {
     "version": "2.0",
     "created": "2026-01-17T15:35:12.024432Z",
-    "modified": "2026-01-20T20:05:28.197219Z",
+    "modified": "2026-01-22T13:48:14.104039Z",
     "created_by": "migration",
-    "modified_by": "test",
+    "modified_by": "canvas",
     "study_name": "m1_mirror_cost_reduction_lateral",
     "description": "Lateral support optimization with new U-joint expressions (lateral_inner_u, lateral_outer_u) for cost reduction model. Focus on WFE and MFG only - no mass objective.",
     "tags": [
@@ -152,22 +152,6 @@
         "y": 580
       }
     },
-    {
-      "name": "variable_1768938898079",
-      "expression_name": "expr_1768938898079",
-      "type": "continuous",
-      "bounds": {
-        "min": 0,
-        "max": 1
-      },
-      "baseline": 0.5,
-      "enabled": true,
-      "canvas_position": {
-        "x": -185.06035488622524,
-        "y": 91.62521000204346
-      },
-      "id": "dv_008"
-    },
     {
       "name": "test_dv",
       "expression_name": "test_expr",
@@ -304,6 +288,27 @@
         "y": 262.2501934501369
       },
       "id": "ext_004"
+    },
+    {
+      "name": "extractor_1769089672375",
+      "type": "custom_function",
+      "builtin": false,
+      "enabled": true,
+      "function": {
+        "name": "extract",
+        "source_code": "def extract(op2_path: str, config: dict = None) -> dict:\n    \"\"\"\n    Custom extractor function.\n    \n    Args:\n        op2_path: Path to the OP2 results file\n        config: Optional configuration dict\n    \n    Returns:\n        Dictionary with extracted values\n    \"\"\"\n    # TODO: Implement extraction logic\n    return {'value': 0.0}\n"
+      },
+      "outputs": [
+        {
+          "name": "value",
+          "metric": "custom"
+        }
+      ],
+      "canvas_position": {
+        "x": 1114.5479601736847,
+        "y": 880.0345512775555
+      },
+      "id": "ext_006"
     }
   ],
   "objectives": [