3 files changed, 97 insertions, 8 deletions

diff --git a/src/src/organizercore.cpp b/src/src/organizercore.cpp
index 810e4c2..6973376 100644
--- a/src/src/organizercore.cpp
+++ b/src/src/organizercore.cpp
@@ -2617,14 +2617,9 @@ bool OrganizerCore::beforeRun(
 

 void OrganizerCore::afterRun(const QFileInfo& binary, DWORD exitCode)

 {

-  // need to remove our stored load order because it may be outdated if a

-  // foreign tool changed the file time. After removing that file,

-  // refreshESPList will use the file time as the order

-  if (managedGame()->loadOrderMechanism() ==

-      IPluginGame::LoadOrderMechanism::FileTime) {

-    log::debug("removing loadorder.txt");

-    QFile::remove(m_CurrentProfile->getLoadOrderFileName());

-  }

+  const bool fileTimeLoadOrder =

+      managedGame()->loadOrderMechanism() ==

+      IPluginGame::LoadOrderMechanism::FileTime;

 

 #ifndef _WIN32

   // Unmount the FUSE VFS now that the application has exited.  unmount()

@@ -2695,11 +2690,34 @@ void OrganizerCore::afterRun(const QFileInfo& binary, DWORD exitCode)
                       prefixPathStr);

           }

         }

+

+        // Sync plugins.txt / loadorder.txt back from the prefix.  LOOT and

+        // similar tools edit the deployed copies in AppData/Local/<Game>/ —

+        // without this sync, their changes are lost when refreshESPList

+        // rereads the untouched profile copy and savePluginList clobbers

+        // them with the old in-memory order.

+        const QString profilePluginsPath = m_CurrentProfile->getPluginsFileName();

+        const QString profileLoadOrderPath =

+            m_CurrentProfile->getLoadOrderFileName();

+        if (!prefix.syncPluginsBack(profilePluginsPath, profileLoadOrderPath,

+                                    dataDirName)) {

+          log::warn("Failed to sync plugins.txt / loadorder.txt back from prefix '{}'",

+                    prefixPathStr);

+        }

       }

     }

   }

 #endif

 

+  // FileTime-based games (Skyrim LE, FO3, FNV) derive the load order from

+  // plugin file mtimes rather than loadorder.txt.  Drop the profile copy so

+  // refreshESPList falls back to file times — LOOT updates those directly

+  // on the .esp files via FUSE setattr.

+  if (fileTimeLoadOrder) {

+    log::debug("removing loadorder.txt (FileTime load order mechanism)");

+    QFile::remove(m_CurrentProfile->getLoadOrderFileName());

+  }

+

   // Refresh directory structure after VFS is unmounted so the refresher

   // reads the real (vanilla) data directory plus individual mod directories,

   // matching Windows USVFS behaviour.

diff --git a/src/src/wineprefix.cpp b/src/src/wineprefix.cpp
index de61172..741855d 100644
--- a/src/src/wineprefix.cpp
+++ b/src/src/wineprefix.cpp
@@ -532,6 +532,70 @@ bool WinePrefix::syncProfileInisBack(
   return allCopied;
 }
 
+bool WinePrefix::syncPluginsBack(const QString& profilePluginsPath,
+                                 const QString& profileLoadOrderPath,
+                                 const QString& dataDir) const
+{
+  if (!isValid()) {
+    MOBase::log::error("syncPluginsBack: prefix '{}' is not valid", m_prefixPath);
+    return false;
+  }
+
+  const QString pluginsDir = QDir(appdataLocal()).filePath(dataDir);
+  if (!QDir(pluginsDir).exists()) {
+    MOBase::log::debug("syncPluginsBack: prefix plugins dir '{}' does not exist",
+                       pluginsDir);
+    return true;
+  }
+
+  auto pickNewest = [&](const QString& canonicalName) -> QString {
+    const QStringList variants =
+        findCaseVariants(QDir(pluginsDir).filePath(canonicalName));
+    QString newest;
+    QDateTime newestTime;
+    for (const QString& v : variants) {
+      const QFileInfo fi(v);
+      if (!newestTime.isValid() || fi.lastModified() > newestTime) {
+        newestTime = fi.lastModified();
+        newest     = v;
+      }
+    }
+    return newest;
+  };
+
+  bool ok = true;
+
+  const QString newestPlugins = pickNewest("plugins.txt");
+  if (!newestPlugins.isEmpty()) {
+    MOBase::log::info("syncPluginsBack: '{}' <- '{}'", profilePluginsPath,
+                      newestPlugins);
+    if (!copyFileWithParents(newestPlugins, profilePluginsPath)) {
+      MOBase::log::error("syncPluginsBack: failed to copy plugins.txt back to '{}'",
+                         profilePluginsPath);
+      ok = false;
+    }
+  } else {
+    MOBase::log::debug("syncPluginsBack: no plugins.txt variant found in '{}'",
+                       pluginsDir);
+  }
+
+  const QString newestLoadOrder = pickNewest("loadorder.txt");
+  if (!newestLoadOrder.isEmpty()) {
+    MOBase::log::info("syncPluginsBack: '{}' <- '{}'", profileLoadOrderPath,
+                      newestLoadOrder);
+    if (!copyFileWithParents(newestLoadOrder, profileLoadOrderPath)) {
+      MOBase::log::error("syncPluginsBack: failed to copy loadorder.txt back to '{}'",
+                         profileLoadOrderPath);
+      ok = false;
+    }
+  } else {
+    MOBase::log::debug("syncPluginsBack: no loadorder.txt variant found in '{}'",
+                       pluginsDir);
+  }
+
+  return ok;
+}
+
 // ── Wine registry (.reg file) access ─────────────────────────────────────────
 
 // Wine .reg files use doubled backslashes in key paths:
diff --git a/src/src/wineprefix.h b/src/src/wineprefix.h
index ac8f0a2..b0e54e7 100644
--- a/src/src/wineprefix.h
+++ b/src/src/wineprefix.h
@@ -32,6 +32,13 @@ public:
   bool syncProfileInisBack(
       const QList<QPair<QString, QString>>& iniMappings) const;
 
+  // Sync plugins.txt / loadorder.txt from the prefix AppData back to the
+  // profile after a tool like LOOT may have edited them.  Picks the newest
+  // case-insensitive variant of each file.
+  bool syncPluginsBack(const QString& profilePluginsPath,
+                       const QString& profileLoadOrderPath,
+                       const QString& dataDir) const;
+
   // Restore any stale .mo2linux_backup INI/save files left by a crash.
   // Should be called at startup before any game runs.
   void restoreStaleBackups() const;