feat: Improve dashboard layout and Claude terminal context

- Reorganize dashboard: control panel on top, charts stacked vertically
- Add Set Context button to Claude terminal for study awareness
- Add conda environment instructions to CLAUDE.md
- Fix STUDY_REPORT.md location in generate-report.md skill
- Claude terminal now sends study context with skills reminder

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

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

atomizer-dashboard/frontend/src/components/ClaudeTerminal.tsx

@@ -9,7 +9,8 @@ import {
   Minimize2,
   X,
   RefreshCw,
-  AlertCircle
+  AlertCircle,
+  FolderOpen
 } from 'lucide-react';
 import { useStudy } from '../context/StudyContext';
 
@@ -33,6 +34,8 @@ export const ClaudeTerminal: React.FC<ClaudeTerminalProps> = ({
   const [isConnecting, setIsConnecting] = useState(false);
   const [_error, setError] = useState<string | null>(null);
   const [cliAvailable, setCliAvailable] = useState<boolean | null>(null);
+  const [contextSet, setContextSet] = useState(false);
+  const [settingContext, setSettingContext] = useState(false);
 
   // Check CLI availability
   useEffect(() => {
@@ -165,8 +168,7 @@ export const ClaudeTerminal: React.FC<ClaudeTerminalProps> = ({
       xtermRef.current?.clear();
       xtermRef.current?.writeln('\x1b[1;32mConnected to Claude Code\x1b[0m');
       if (selectedStudy?.id) {
-        xtermRef.current?.writeln(`\x1b[90mStudy context: \x1b[1;33m${selectedStudy.id}\x1b[0m`);
-        xtermRef.current?.writeln('\x1b[90mTip: Tell Claude about your study, e.g. "Help me with study ' + selectedStudy.id + '"\x1b[0m');
+        xtermRef.current?.writeln(`\x1b[90mStudy: \x1b[1;33m${selectedStudy.id}\x1b[0m \x1b[90m- Click "Set Context" to initialize\x1b[0m`);
       }
       xtermRef.current?.writeln('');
 
@@ -241,8 +243,26 @@ export const ClaudeTerminal: React.FC<ClaudeTerminalProps> = ({
       wsRef.current = null;
     }
     setIsConnected(false);
+    setContextSet(false);
   }, []);
 
+  // Set study context - sends context message to Claude silently
+  const setStudyContext = useCallback(() => {
+    if (!wsRef.current || wsRef.current.readyState !== WebSocket.OPEN || !selectedStudy?.id) return;
+
+    setSettingContext(true);
+    // Send context message - Claude should use CLAUDE.md and .claude/skills/ for guidance
+    const contextMessage = `Context: Working on study "${selectedStudy.id}" at studies/${selectedStudy.id}/. ` +
+      `Read .claude/skills/ for task protocols. Use atomizer conda env. Acknowledge briefly.`;
+    wsRef.current.send(JSON.stringify({ type: 'input', data: contextMessage + '\n' }));
+
+    // Mark as done after Claude has had time to process
+    setTimeout(() => {
+      setSettingContext(false);
+      setContextSet(true);
+    }, 500);
+  }, [selectedStudy]);
+
   // Cleanup on unmount
   useEffect(() => {
     return () => {
@@ -293,6 +313,35 @@ export const ClaudeTerminal: React.FC<ClaudeTerminalProps> = ({
             {isConnected ? 'Disconnect' : 'Connect'}
           </button>
 
+          {/* Set Context button - always show, with different states */}
+          <button
+            onClick={setStudyContext}
+            disabled={!selectedStudy?.id || !isConnected || settingContext || contextSet}
+            className={`px-3 py-1.5 text-sm rounded-lg transition-colors flex items-center gap-2 ${
+              contextSet
+                ? 'bg-green-600/20 text-green-400'
+                : !selectedStudy?.id || !isConnected
+                  ? 'bg-dark-600 text-dark-400'
+                  : 'bg-primary-600/20 text-primary-400 hover:bg-primary-600/30'
+            } disabled:opacity-50 disabled:cursor-not-allowed`}
+            title={
+              !selectedStudy?.id
+                ? 'No study selected - select a study from Home page'
+                : !isConnected
+                  ? 'Connect first to set study context'
+                  : contextSet
+                    ? 'Context already set'
+                    : `Set context to study: ${selectedStudy.id}`
+            }
+          >
+            {settingContext ? (
+              <RefreshCw className="w-3 h-3 animate-spin" />
+            ) : (
+              <FolderOpen className="w-3 h-3" />
+            )}
+            {contextSet ? 'Context Set' : selectedStudy?.id ? 'Set Context' : 'No Study'}
+          </button>
+
           {onToggleExpand && (
             <button
               onClick={onToggleExpand}