auto: 2026-06-10_06:00 changes

1 files changed, 42 insertions, 2 deletions

diff --git a/modules/core/module-neural-vfs.js b/modules/core/module-neural-vfs.js
index bdf1ffb..613d53a 100644
--- a/modules/core/module-neural-vfs.js
+++ b/modules/core/module-neural-vfs.js
@@ -7,6 +7,7 @@ class NeuralVFSModule {
             'nvfs-tree': { argType: 'file' }, 'nvfs-config': { argType: 'file' },
             'nvfs-alias': { argType: 'file' },
             'nvfs-sync': { argType: 'file' },
+            'nvfs-save': { argType: 'none' },
         };
         this.terminal = null;
         this.index = {};
@@ -55,7 +56,8 @@ class NeuralVFSModule {
             'nvfs-tree': 'nvfs-tree [concept] — Show concept-to-file mapping as a tree',
             'nvfs-config': 'nvfs-config [key] [value] — View or set Neural VFS config (fuzzy-limit, tree-files, tree-concepts, resolve-files, deep-index, deep-model)',
             'nvfs-alias': 'nvfs-alias list|add|remove|clear — Manage concept aliases',
-            'nvfs-sync': 'nvfs-sync [--deep] — Incremental background sync (auto-sync dirty files)'
+            'nvfs-sync': 'nvfs-sync [--deep] — Incremental background sync (auto-sync dirty files)',
+            'nvfs-save': 'nvfs-save — Force-save current in-memory index to VFS (survives refresh)'
         };
     }
 
@@ -67,6 +69,7 @@ class NeuralVFSModule {
         this.commands['nvfs-config'] = (args) => this.nvfsConfig(args);
         this.commands['nvfs-alias'] = (args) => this.nvfsAlias(args);
         this.commands['nvfs-sync'] = async (args) => this.nvfsSync(args);
+        this.commands['nvfs-save'] = (args) => this.nvfsSave();
     }
 
     // ── Core Index Builder (async, chunked) ──
@@ -76,6 +79,19 @@ class NeuralVFSModule {
         const fs = this.terminal.fs;
         if (!fs) return this.terminal.print('VFS not available', 'error');
 
+        // Safety guard: warn if deep mode is off but the saved index has LLM concepts
+        if (!useDeep) {
+            const prevIndex = fs.fsReadJSON(this.indexPath) || {};
+            const hasLLM = Object.values(prevIndex).some(entries =>
+                Array.isArray(entries) && entries.some(e => e.source === 'llm')
+            );
+            if (hasLLM) {
+                this.terminal.print('⚠️  Deep indexing is OFF but the saved index contains LLM-generated concepts.', 'warning');
+                this.terminal.print('   Running nvfs-index without --deep will STRIP all LLM concepts from re-indexed files.', 'warning');
+                this.terminal.print('   To keep them: nvfs-config deep-index on  or  nvfs-index --deep', 'warning');
+            }
+        }
+
         this.terminal.print(`🔍 Scanning VFS for semantic concepts${useDeep ? ' (deep mode)' : ''}...`, 'info');
 
         const start = Date.now();
@@ -634,7 +650,7 @@ class NeuralVFSModule {
                 const hash = this._contentHash(content);
                 const cached = this._getCached(path, hash);
                 if (!cached) {
-                    this._reindexFile(path, content, this.index);
+                    this._reindexFile(path, content, this.index, this._deepIndexEnabled);
                     this._hashCache[path] = { hash };
                     reindexed++;
                 }
@@ -768,6 +784,30 @@ Concepts:`;
             const llmConcepts = results.reduce((s, r) => s + r.concepts.length, 0);
             this.terminal?.print(`🧠 Deep pass complete: ${llmConcepts} LLM-generated concepts across ${results.length} files`, 'success');
         }
+        // Persist LLM-generated concepts to disk so they survive page refresh
+        // Must force-save because _saveIndex() calls saveToStorage() which has a
+        // debounce guard (_storageSavePending) that may still be set from the
+        // initial buildIndex() save — without clearing it, the LLM concepts are
+        // never written to localStorage and are lost on page refresh.
+        const vfs = this.terminal?.fs;
+        if (vfs) {
+            vfs._storageSavePending = false;
+            this._saveIndex(vfs);
+        }
+    }
+
+    // ── Nvfs Save (force-persist in-memory index) ──
+
+    nvfsSave() {
+        const fs = this.terminal?.fs;
+        if (!fs) return this.terminal?.print('VFS not available', 'error');
+        const count = Object.keys(this.index).length;
+        if (count === 0) return this.terminal?.print('No index in memory to save', 'warning');
+        // Bypass debounce guard to ensure write
+        fs._storageSavePending = false;
+        this._saveIndex(fs);
+        this.terminal?.print(`✅ Saved ${count} concepts to ${this.indexPath}`, 'success');
+        this.terminal?.print('   Index will survive page refresh', 'info');
     }
 
     // ── Nvfs Sync (incremental background) ──