fix(newos4): the virtual /sys entry leaked into listings, trees and counts (v4.6.88-90)

One phantom entry, three symptoms:
- ls() injected 'sys' whenever it was called without a path, so 'cd _agents; ls' advertised a
  sys directory that does not exist, and list_files('_agents/sys') answered 'Directory not
  found' — the reported false negative. Injection is now gated on dir === root.
- tree() pushed the same virtual name into the walk and dereferenced it, throwing mid-output on
  every root listing. Guarded.
- _gatherFileInfo() walked into /sys and counted a synthetic subtree: 146 files / 114 dirs for a
  44-file / 15-dir store. Virtual entries are skipped.

Verified: root still lists sys; _agents and skills do not; tree('') completes; world model total
(44) equals an independent walk of fs.root (44), agree: true.

4 files changed, 45 insertions, 13 deletions

diff --git a/modules/core/core-bundle.js b/modules/core/core-bundle.js
index c8a4c2e..f72a20e 100644
--- a/modules/core/core-bundle.js
+++ b/modules/core/core-bundle.js
@@ -548,8 +548,11 @@ class VirtualFileSystem {
             size: dir.content[name]._factory ? 0 : (dir.content[name].content ? dir.content[name].content.length : 0),
             _virtual: !!dir.content[name]._virtual
         }));
-        // Inject virtual /sys/ at root level
-        if ((!path || path === '/' || path === '') && !entries.some(e => e.name === 'sys' && e._virtual)) {
+        // Inject virtual /sys/ — but ONLY when the directory being listed IS the root.
+        // The old test was on the argument (`!path`), not on the result: `cd _agents; ls`
+        // printed a phantom `sys` inside _agents, and a follow-up list_files('_agents/sys')
+        // failed with 'Directory not found'. The listing lied; the resolver was right.
+        if (dir === this.root && !entries.some(e => e.name === 'sys' && e._virtual)) {
             entries.push({ name: 'sys', type: 'dir', size: 0, _virtual: true });
         }
         return entries;
@@ -765,8 +768,11 @@ class VirtualFileSystem {
             size: dir.content[name]._factory ? 0 : (dir.content[name].content ? dir.content[name].content.length : 0),
             _virtual: !!dir.content[name]._virtual
         }));
-        // Inject virtual /sys/ at root level
-        if ((!path || path === '/' || path === '') && !entries.some(e => e.name === 'sys' && e._virtual)) {
+        // Inject virtual /sys/ — but ONLY when the directory being listed IS the root.
+        // The old test was on the argument (`!path`), not on the result: `cd _agents; ls`
+        // printed a phantom `sys` inside _agents, and a follow-up list_files('_agents/sys')
+        // failed with 'Directory not found'. The listing lied; the resolver was right.
+        if (dir === this.root && !entries.some(e => e.name === 'sys' && e._virtual)) {
             entries.push({ name: 'sys', type: 'dir', size: 0, _virtual: true });
         }
         return entries;
@@ -804,9 +810,14 @@ class VirtualFileSystem {
             const isLast = i === entries.length - 1;
             const connector = isLast ? '└── ' : '├── ';
             result += prefix + connector + name + '\n';
-            if (dir.content[name].type === 'dir' || dir.content[name]._virtual) {
+            // The loop pushes the virtual 'sys' name into `entries`, which has no node behind it:
+            // dereferencing dir.content['sys'].type threw 'Cannot read properties of undefined'
+            // and `tree` died on the root listing — often after printing a partial tree, which is
+            // where the disagreeing file counts came from.
+            const child = dir.content[name];
+            if (child && child.type === 'dir') {
                 const ext = isLast ? '    ' : '│   ';
-                result += this.tree(path + '/' + name, prefix + ext);
+                result += this.tree((path || '') + '/' + name, prefix + ext);
             }
         }
         return result;
@@ -18814,6 +18825,11 @@ class WorldModelModule {
             const entries = fs.ls(path);
             if (!entries) return;
             for (const e of entries) {
+                // /sys is synthesized by ls() on demand and has no node behind it. Walking into it
+                // counted a synthetic subtree (114 dirs / 146 files in a store that holds 43 files),
+                // which is the "the counts disagree" report: two different populations were both
+                // printed as "files".
+                if (e._virtual) continue;
                 if (e.type === 'file') fileCount++;
                 else { dirCount++; walk(path === '/' ? '/' + e.name : path + '/' + e.name); }
             }
diff --git a/modules/core/module-loader.js b/modules/core/module-loader.js
index 37212f3..95176d9 100644
--- a/modules/core/module-loader.js
+++ b/modules/core/module-loader.js
@@ -4,7 +4,7 @@
     // Core module bundle loaded synchronously in main.html.
     // This loader only handles version cache-busting, splash, terminal init, and optional ext modules.
 
-    const LATEST_VER = 'v4.6.87';
+    const LATEST_VER = 'v4.6.90';
     const CACHE = '?v=' + LATEST_VER;
     const stored = localStorage.getItem('webx11_cache_ver');
     if (stored !== LATEST_VER) {
diff --git a/modules/core/module-world-model.js b/modules/core/module-world-model.js
index 54a17e4..6e8f3c3 100644
--- a/modules/core/module-world-model.js
+++ b/modules/core/module-world-model.js
@@ -203,6 +203,11 @@ class WorldModelModule {
             const entries = fs.ls(path);
             if (!entries) return;
             for (const e of entries) {
+                // /sys is synthesized by ls() on demand and has no node behind it. Walking into it
+                // counted a synthetic subtree (114 dirs / 146 files in a store that holds 43 files),
+                // which is the "the counts disagree" report: two different populations were both
+                // printed as "files".
+                if (e._virtual) continue;
                 if (e.type === 'file') fileCount++;
                 else { dirCount++; walk(path === '/' ? '/' + e.name : path + '/' + e.name); }
             }
diff --git a/modules/core/virtual-fs.js b/modules/core/virtual-fs.js
index a52a393..e639cba 100644
--- a/modules/core/virtual-fs.js
+++ b/modules/core/virtual-fs.js
@@ -546,8 +546,11 @@ class VirtualFileSystem {
             size: dir.content[name]._factory ? 0 : (dir.content[name].content ? dir.content[name].content.length : 0),
             _virtual: !!dir.content[name]._virtual
         }));
-        // Inject virtual /sys/ at root level
-        if ((!path || path === '/' || path === '') && !entries.some(e => e.name === 'sys' && e._virtual)) {
+        // Inject virtual /sys/ — but ONLY when the directory being listed IS the root.
+        // The old test was on the argument (`!path`), not on the result: `cd _agents; ls`
+        // printed a phantom `sys` inside _agents, and a follow-up list_files('_agents/sys')
+        // failed with 'Directory not found'. The listing lied; the resolver was right.
+        if (dir === this.root && !entries.some(e => e.name === 'sys' && e._virtual)) {
             entries.push({ name: 'sys', type: 'dir', size: 0, _virtual: true });
         }
         return entries;
@@ -763,8 +766,11 @@ class VirtualFileSystem {
             size: dir.content[name]._factory ? 0 : (dir.content[name].content ? dir.content[name].content.length : 0),
             _virtual: !!dir.content[name]._virtual
         }));
-        // Inject virtual /sys/ at root level
-        if ((!path || path === '/' || path === '') && !entries.some(e => e.name === 'sys' && e._virtual)) {
+        // Inject virtual /sys/ — but ONLY when the directory being listed IS the root.
+        // The old test was on the argument (`!path`), not on the result: `cd _agents; ls`
+        // printed a phantom `sys` inside _agents, and a follow-up list_files('_agents/sys')
+        // failed with 'Directory not found'. The listing lied; the resolver was right.
+        if (dir === this.root && !entries.some(e => e.name === 'sys' && e._virtual)) {
             entries.push({ name: 'sys', type: 'dir', size: 0, _virtual: true });
         }
         return entries;
@@ -802,9 +808,14 @@ class VirtualFileSystem {
             const isLast = i === entries.length - 1;
             const connector = isLast ? '└── ' : '├── ';
             result += prefix + connector + name + '\n';
-            if (dir.content[name].type === 'dir' || dir.content[name]._virtual) {
+            // The loop pushes the virtual 'sys' name into `entries`, which has no node behind it:
+            // dereferencing dir.content['sys'].type threw 'Cannot read properties of undefined'
+            // and `tree` died on the root listing — often after printing a partial tree, which is
+            // where the disagreeing file counts came from.
+            const child = dir.content[name];
+            if (child && child.type === 'dir') {
                 const ext = isLast ? '    ' : '│   ';
-                result += this.tree(path + '/' + name, prefix + ext);
+                result += this.tree((path || '') + '/' + name, prefix + ext);
             }
         }
         return result;