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>

atomizer-dashboard/backend/api/routes/optimization.py

@@ -245,17 +245,45 @@ def _get_study_error_info(study_dir: Path, results_dir: Path) -> dict:
 
 def _load_study_info(study_dir: Path, topic: Optional[str] = None) -> Optional[dict]:
     """Load study info from a study directory. Returns None if not a valid study."""
-    # Look for optimization config (check multiple locations)
-    config_file = study_dir / "optimization_config.json"
-    if not config_file.exists():
-        config_file = study_dir / "1_setup" / "optimization_config.json"
-    if not config_file.exists():
+    # Look for config file - prefer atomizer_spec.json (v2.0), fall back to legacy optimization_config.json
+    config_file = None
+    is_atomizer_spec = False
+
+    # Check for AtomizerSpec v2.0 first
+    for spec_path in [
+        study_dir / "atomizer_spec.json",
+        study_dir / "1_setup" / "atomizer_spec.json",
+    ]:
+        if spec_path.exists():
+            config_file = spec_path
+            is_atomizer_spec = True
+            break
+
+    # Fall back to legacy optimization_config.json
+    if config_file is None:
+        for legacy_path in [
+            study_dir / "optimization_config.json",
+            study_dir / "1_setup" / "optimization_config.json",
+        ]:
+            if legacy_path.exists():
+                config_file = legacy_path
+                break
+
+    if config_file is None:
         return None
 
     # Load config
     with open(config_file) as f:
         config = json.load(f)
 
+    # Normalize AtomizerSpec v2.0 to legacy format for compatibility
+    if is_atomizer_spec and "meta" in config:
+        # Extract study_name and description from meta
+        meta = config.get("meta", {})
+        config["study_name"] = meta.get("study_name", study_dir.name)
+        config["description"] = meta.get("description", "")
+        config["version"] = meta.get("version", "2.0")
+
     # Check if results directory exists (support both 2_results and 3_results)
     results_dir = study_dir / "2_results"
     if not results_dir.exists():
@@ -311,12 +339,21 @@ def _load_study_info(study_dir: Path, topic: Optional[str] = None) -> Optional[d
                 best_trial = min(history, key=lambda x: x["objective"])
                 best_value = best_trial["objective"]
 
-    # Get total trials from config (supports both formats)
-    total_trials = (
-        config.get("optimization_settings", {}).get("n_trials")
-        or config.get("optimization", {}).get("n_trials")
-        or config.get("trials", {}).get("n_trials", 50)
-    )
+    # Get total trials from config (supports AtomizerSpec v2.0 and legacy formats)
+    total_trials = None
+
+    # AtomizerSpec v2.0: optimization.budget.max_trials
+    if is_atomizer_spec:
+        total_trials = config.get("optimization", {}).get("budget", {}).get("max_trials")
+
+    # Legacy formats
+    if total_trials is None:
+        total_trials = (
+            config.get("optimization_settings", {}).get("n_trials")
+            or config.get("optimization", {}).get("n_trials")
+            or config.get("optimization", {}).get("max_trials")
+            or config.get("trials", {}).get("n_trials", 100)
+        )
 
     # Get accurate status using process detection
     status = get_accurate_study_status(study_dir.name, trial_count, total_trials, has_db)
@@ -380,7 +417,12 @@ async def list_studies():
                 continue
 
             # Check if this is a study (flat structure) or a topic folder (nested structure)
-            is_study = (item / "1_setup").exists() or (item / "optimization_config.json").exists()
+            # Support both AtomizerSpec v2.0 (atomizer_spec.json) and legacy (optimization_config.json)
+            is_study = (
+                (item / "1_setup").exists()
+                or (item / "atomizer_spec.json").exists()
+                or (item / "optimization_config.json").exists()
+            )
 
             if is_study:
                 # Flat structure: study directly in studies/
@@ -396,10 +438,12 @@ async def list_studies():
                     if sub_item.name.startswith("."):
                         continue
 
-                    # Check if this subdirectory is a study
-                    sub_is_study = (sub_item / "1_setup").exists() or (
-                        sub_item / "optimization_config.json"
-                    ).exists()
+                    # Check if this subdirectory is a study (AtomizerSpec v2.0 or legacy)
+                    sub_is_study = (
+                        (sub_item / "1_setup").exists()
+                        or (sub_item / "atomizer_spec.json").exists()
+                        or (sub_item / "optimization_config.json").exists()
+                    )
                     if sub_is_study:
                         study_info = _load_study_info(sub_item, topic=item.name)
                         if study_info: