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>

optimization_engine/schemas/atomizer_spec_v2.json

@@ -85,7 +85,7 @@
         "created_by": {
           "type": "string",
           "description": "Who/what created the spec",
-          "enum": ["canvas", "claude", "api", "migration", "manual"]
+          "enum": ["canvas", "claude", "api", "migration", "manual", "dashboard_intake"]
         },
         "modified_by": {
           "type": "string",
@@ -114,6 +114,17 @@
         "engineering_context": {
           "type": "string",
           "description": "Real-world engineering scenario"
+        },
+        "status": {
+          "type": "string",
+          "description": "Study lifecycle status",
+          "enum": ["draft", "introspected", "configured", "validated", "ready", "running", "completed", "failed"],
+          "default": "draft"
+        },
+        "topic": {
+          "type": "string",
+          "description": "Topic folder for grouping related studies",
+          "pattern": "^[A-Za-z0-9_]+$"
         }
       }
     },
@@ -215,6 +226,124 @@
               "type": "boolean"
             }
           }
+        },
+        "introspection": {
+          "$ref": "#/definitions/introspection_data",
+          "description": "Model introspection results from intake workflow"
+        }
+      }
+    },
+
+    "introspection_data": {
+      "type": "object",
+      "description": "Model introspection results stored in the spec",
+      "properties": {
+        "timestamp": {
+          "type": "string",
+          "format": "date-time",
+          "description": "When introspection was run"
+        },
+        "solver_type": {
+          "type": "string",
+          "description": "Detected solver type"
+        },
+        "mass_kg": {
+          "type": "number",
+          "description": "Mass from expressions or mass properties"
+        },
+        "volume_mm3": {
+          "type": "number",
+          "description": "Volume from mass properties"
+        },
+        "expressions": {
+          "type": "array",
+          "description": "Discovered NX expressions",
+          "items": {
+            "$ref": "#/definitions/expression_info"
+          }
+        },
+        "baseline": {
+          "$ref": "#/definitions/baseline_data",
+          "description": "Baseline FEA solve results"
+        },
+        "warnings": {
+          "type": "array",
+          "description": "Warnings from introspection",
+          "items": {
+            "type": "string"
+          }
+        }
+      }
+    },
+
+    "expression_info": {
+      "type": "object",
+      "description": "Information about an NX expression from introspection",
+      "required": ["name"],
+      "properties": {
+        "name": {
+          "type": "string",
+          "description": "Expression name in NX"
+        },
+        "value": {
+          "type": "number",
+          "description": "Current value"
+        },
+        "units": {
+          "type": "string",
+          "description": "Physical units"
+        },
+        "formula": {
+          "type": "string",
+          "description": "Expression formula if any"
+        },
+        "is_candidate": {
+          "type": "boolean",
+          "description": "Whether this is a design variable candidate",
+          "default": false
+        },
+        "confidence": {
+          "type": "number",
+          "description": "Confidence that this is a design variable (0.0 to 1.0)",
+          "minimum": 0,
+          "maximum": 1
+        }
+      }
+    },
+
+    "baseline_data": {
+      "type": "object",
+      "description": "Results from baseline FEA solve",
+      "properties": {
+        "timestamp": {
+          "type": "string",
+          "format": "date-time",
+          "description": "When baseline was run"
+        },
+        "solve_time_seconds": {
+          "type": "number",
+          "description": "How long the solve took"
+        },
+        "mass_kg": {
+          "type": "number",
+          "description": "Computed mass from BDF/FEM"
+        },
+        "max_displacement_mm": {
+          "type": "number",
+          "description": "Max displacement result"
+        },
+        "max_stress_mpa": {
+          "type": "number",
+          "description": "Max von Mises stress"
+        },
+        "success": {
+          "type": "boolean",
+          "description": "Whether baseline solve succeeded",
+          "default": true
+        },
+        "error": {
+          "type": "string",
+          "description": "Error message if failed"
         }
       }
     },