feat: Dashboard improvements and configuration updates

Dashboard:
- Enhanced terminal components (ClaudeTerminal, GlobalClaudeTerminal)
- Improved MarkdownRenderer for better documentation display
- Updated convergence plots (ConvergencePlot, PlotlyConvergencePlot)
- Refined Home, Analysis, Dashboard, Setup, Results pages
- Added StudyContext improvements
- Updated vite.config for better dev experience

Configuration:
- Updated CLAUDE.md with latest instructions
- Enhanced launch_dashboard.py
- Updated config.py settings

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

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

@@ -20,9 +20,43 @@ router = APIRouter()
 _terminal_sessions: dict = {}
 
 # Path to Atomizer root (for loading prompts)
-ATOMIZER_ROOT = os.path.dirname(os.path.dirname(os.path.dirname(
-    os.path.dirname(os.path.dirname(os.path.abspath(__file__)))
-)))
+# Go up 5 levels: terminal.py -> routes -> api -> backend -> atomizer-dashboard -> Atomizer
+_file_path = os.path.abspath(__file__)
+ATOMIZER_ROOT = os.path.normpath(os.path.dirname(os.path.dirname(os.path.dirname(
+    os.path.dirname(os.path.dirname(_file_path))
+))))
+STUDIES_DIR = os.path.join(ATOMIZER_ROOT, "studies")
+# Debug: print the resolved path at module load
+print(f"[Terminal] ATOMIZER_ROOT resolved to: {ATOMIZER_ROOT}")
+
+
+def resolve_study_path(study_id: str) -> str:
+    """Find study folder by scanning topic directories.
+
+    Returns relative path from ATOMIZER_ROOT (e.g., 'studies/M1_Mirror/m1_mirror_adaptive_V14').
+    """
+    # First check direct path (flat structure)
+    direct_path = os.path.join(STUDIES_DIR, study_id)
+    if os.path.isdir(direct_path):
+        setup_dir = os.path.join(direct_path, "1_setup")
+        config_file = os.path.join(direct_path, "optimization_config.json")
+        if os.path.exists(setup_dir) or os.path.exists(config_file):
+            return f"studies/{study_id}"
+
+    # Scan topic folders for nested structure
+    if os.path.isdir(STUDIES_DIR):
+        for topic_name in os.listdir(STUDIES_DIR):
+            topic_path = os.path.join(STUDIES_DIR, topic_name)
+            if os.path.isdir(topic_path) and not topic_name.startswith('.'):
+                study_path = os.path.join(topic_path, study_id)
+                if os.path.isdir(study_path):
+                    setup_dir = os.path.join(study_path, "1_setup")
+                    config_file = os.path.join(study_path, "optimization_config.json")
+                    if os.path.exists(setup_dir) or os.path.exists(config_file):
+                        return f"studies/{topic_name}/{study_id}"
+
+    # Fallback to flat path
+    return f"studies/{study_id}"
 
 
 def get_session_prompt(study_name: str = None) -> str:
@@ -54,19 +88,21 @@ def get_session_prompt(study_name: str = None) -> str:
     ]
 
     if study_name:
+        # Resolve actual study path (handles nested folder structure)
+        study_path = resolve_study_path(study_name)
         prompt_lines.extend([
             f"## Current Study: `{study_name}`",
             "",
-            f"**Directory**: `studies/{study_name}/`",
+            f"**Directory**: `{study_path}/`",
             "",
             "Key files:",
-            f"- `studies/{study_name}/1_setup/optimization_config.json` - Configuration",
-            f"- `studies/{study_name}/2_results/study.db` - Optuna database",
-            f"- `studies/{study_name}/README.md` - Study documentation",
+            f"- `{study_path}/1_setup/optimization_config.json` - Configuration",
+            f"- `{study_path}/3_results/study.db` - Optuna database",
+            f"- `{study_path}/README.md` - Study documentation",
             "",
             "Quick status check:",
             "```bash",
-            f"python -c \"import optuna; s=optuna.load_study('{study_name}', 'sqlite:///studies/{study_name}/2_results/study.db'); print(f'Trials: {{len(s.trials)}}, Best: {{s.best_value}}')\"",
+            f"python -c \"import optuna; s=optuna.load_study('{study_name}', 'sqlite:///{study_path}/3_results/study.db'); print(f'Trials: {{len(s.trials)}}, Best: {{s.best_value}}')\"",
             "```",
             "",
         ])
@@ -99,8 +135,10 @@ def get_session_prompt(study_name: str = None) -> str:
 try:
     from winpty import PtyProcess
     HAS_WINPTY = True
-except ImportError:
+    print("[Terminal] winpty is available")
+except ImportError as e:
     HAS_WINPTY = False
+    print(f"[Terminal] winpty not available: {e}")
 
 
 class TerminalSession:
@@ -120,6 +158,15 @@ class TerminalSession:
         self.websocket = websocket
         self._running = True
 
+        # Validate working directory exists
+        if not os.path.isdir(self.working_dir):
+            await self.websocket.send_json({
+                "type": "error",
+                "message": f"Working directory does not exist: {self.working_dir}"
+            })
+            self._running = False
+            return
+
         try:
             if self._use_winpty:
                 # Use winpty for proper PTY on Windows
@@ -143,7 +190,8 @@ class TerminalSession:
                 )
             elif sys.platform == "win32":
                 # Fallback: Windows without winpty - use subprocess
-                # Run claude with --dangerously-skip-permissions for non-interactive mode
+                import shutil
+                claude_cmd = shutil.which("claude") or "claude"
                 self.process = subprocess.Popen(
                     ["cmd.exe", "/k", claude_cmd],
                     stdin=subprocess.PIPE,
@@ -157,6 +205,8 @@ class TerminalSession:
             else:
                 # On Unix, use pty
                 import pty
+                import shutil
+                claude_cmd = shutil.which("claude") or "claude"
                 master_fd, slave_fd = pty.openpty()
                 self.process = subprocess.Popen(
                     [claude_cmd],
@@ -467,6 +517,9 @@ async def get_context(study_id: str = None):
     """
     prompt = get_session_prompt(study_id)
 
+    # Resolve study path for nested folder structure
+    study_path = resolve_study_path(study_id) if study_id else None
+
     return {
         "study_id": study_id,
         "prompt": prompt,
@@ -476,8 +529,8 @@ async def get_context(study_id: str = None):
             ".claude/skills/02_CONTEXT_LOADER.md",
         ],
         "study_files": [
-            f"studies/{study_id}/1_setup/optimization_config.json",
-            f"studies/{study_id}/2_results/study.db",
-            f"studies/{study_id}/README.md",
-        ] if study_id else []
+            f"{study_path}/1_setup/optimization_config.json",
+            f"{study_path}/3_results/study.db",
+            f"{study_path}/README.md",
+        ] if study_path else []
     }