Fix PLUMED: use session-aware API for generate/preview; add update note on Protein Loading

ambermdflow/html/index.html

@@ -53,7 +53,9 @@
             <div id="protein-loading" class="tab-content active">
                 <div class="card">
                     <h2><i class="fas fa-dna"></i> Protein Structure Input</h2>
-                    
+                    <p class="card-description" style="margin-bottom: 0.5rem; padding: 0.5rem 0.75rem; background: #e8f4fd; border-left: 4px solid #007bff; border-radius: 4px; font-size: 0.95rem;">
+                        <i class="fas fa-info-circle"></i> <strong>Update:</strong> PLUMED section is fixed — saving <code>plumed.dat</code> and generating/previewing simulation files now work correctly.
+                    </p>
                     <div class="input-methods">
                         <div class="method-option">
                             <h3><i class="fas fa-file-upload"></i> Upload PDB File</h3>

ambermdflow/js/plumed.js

@@ -2599,9 +2599,9 @@ ves: VES ARG=distance SIGMA=0.1 PACE=500`,
     }
 
     async generatePlumedFiles() {
-        // Check if plumed.dat exists
+        // Check if plumed.dat exists via API (use plumedApiFetch so same session as save is used)
         try {
-            const checkResponse = await fetch('/output/plumed.dat', { method: 'HEAD' });
+            const checkResponse = await plumedApiFetch('/api/get-file?filename=plumed.dat', { cache: 'no-store' });
             if (!checkResponse.ok) {
                 alert('Please save a PLUMED file (plumed.dat) first before generating simulation files.');
                 return;
@@ -2678,9 +2678,9 @@ ves: VES ARG=distance SIGMA=0.1 PACE=500`,
     }
 
     async previewPlumedFiles() {
-        // Use the same preview functionality as section 6, but include plumed.dat
+        // Use the same preview functionality as section 6, but include plumed.dat (use session-aware API)
         try {
-            const resp = await fetch('/api/get-generated-files');
+            const resp = await plumedApiFetch('/api/get-generated-files');
             const data = await resp.json();
             if (!data.success) {
                 alert('❌ Error: ' + (data.error || 'Unable to load files'));