Replace Python plugins with native C++ .so, remove bundled Python (~95MB)

- Add native plugins: form43_checker, script_extender_checker, preview_dds,
  basic_games (75 game defs via IPluginProxy pattern with Steam/GOG detection)
- Remove portable Python from Dockerfile and build-inner.sh
- Add Python settings tab with venv support (system python3 + PyQt6)
- Skip loading plugin_python.so when Python disabled (default: off)
- Update pythonrunner.cpp to use venv at ~/.local/share/fluorine/python-venv/
- Preserve real file permissions in FUSE VFS (fixes native executable +x bits)
- Add FUSE_SET_ATTR_MODE handler so chmod works through VFS
- Fix desktop shortcut Exec= to use fluorine-manager launcher, not bare binary

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

9 files changed, 503 insertions, 32 deletions

diff --git a/src/src/CMakeLists.txt b/src/src/CMakeLists.txt
index d7a7642..30dd8b5 100644
--- a/src/src/CMakeLists.txt
+++ b/src/src/CMakeLists.txt
@@ -121,7 +121,7 @@ target_compile_definitions(organizer PRIVATE
 if(NOT WIN32)
     option(MO2_BUNDLE_7Z_RUNTIME "Copy a Linux 7z module into organizer/dlls" ON)
     option(MO2_STAGE_PYTHON_PLUGIN_PAYLOAD
-        "Stage shipped Python plugin payload into build plugins/ for Linux runs" ON)
+        "Stage shipped Python plugin payload into build plugins/ for Linux runs" OFF)
     option(MO2_STAGE_INSTALLER_WIZARD
         "Stage installer_wizard python plugin payload (requires additional wizard package)" OFF)
     set(MO2_7Z_SO_PATH "" CACHE FILEPATH
diff --git a/src/src/envshortcut.cpp b/src/src/envshortcut.cpp
index e78e904..5b6ff8e 100644
--- a/src/src/envshortcut.cpp
+++ b/src/src/envshortcut.cpp
@@ -377,6 +377,14 @@ static QString appImageOrBinary()
   if (!appImage.isEmpty() && QFile::exists(appImage)) {

     return appImage;

   }

+  // Prefer the fluorine-manager launcher script over the bare ModOrganizer-core

+  // binary — the launcher sets up bundled library paths, Qt plugin paths, etc.

+  // Without it, shortcuts fail on systems that don't have all deps in PATH.

+  const QString appDir = QCoreApplication::applicationDirPath();

+  const QString launcher = appDir + "/fluorine-manager";

+  if (QFile::exists(launcher)) {

+    return QFileInfo(launcher).absoluteFilePath();

+  }

   return QFileInfo(qApp->applicationFilePath()).absoluteFilePath();

 }

 

diff --git a/src/src/plugincontainer.cpp b/src/src/plugincontainer.cpp
index e215c0a..a170c99 100644
--- a/src/src/plugincontainer.cpp
+++ b/src/src/plugincontainer.cpp
@@ -9,6 +9,7 @@
 #include <QDirIterator>

 #include <QMessageBox>

 #include <QToolButton>

+#include <QSettings>

 #include <cstdio>

 #include <boost/fusion/algorithm/iteration/for_each.hpp>

 #include <boost/fusion/include/at_key.hpp>

@@ -1304,6 +1305,17 @@ void PluginContainer::loadPlugins()
       }

     }

 

+    // Skip the Python proxy plugin unless the user has enabled Python support

+    // in Settings > Python. Native C++ replacements handle all default plugins.

+    if (iter.fileName() == "libplugin_python.so" ||

+        iter.fileName() == "plugin_python.dll") {

+      if (!QSettings().value("fluorine/python_enabled", false).toBool()) {

+        log::debug("plugin \"{}\" skipped (Python plugins disabled in settings)",

+                   iter.fileName());

+        continue;

+      }

+    }

+

     if (loadCheck.isOpen()) {

       loadCheck.write(iter.fileName().toUtf8());

       loadCheck.write("\n");

diff --git a/src/src/settingsdialog.cpp b/src/src/settingsdialog.cpp
index 919bf4e..757c6f8 100644
--- a/src/src/settingsdialog.cpp
+++ b/src/src/settingsdialog.cpp
@@ -21,12 +21,13 @@ along with Mod Organizer.  If not, see <http://www.gnu.org/licenses/>.
 #include "settingsdialogdiagnostics.h"

 #include "settingsdialoggeneral.h"

 #include "settingsdialogmodlist.h"

-#include "settingsdialognexus.h"
-#include "settingsdialogpaths.h"
-#include "settingsdialogplugins.h"
-#include "settingsdialogproton.h"
-#include "settingsdialogtheme.h"
-#include "settingsdialogworkarounds.h"
+#include "settingsdialognexus.h"

+#include "settingsdialogpaths.h"

+#include "settingsdialogplugins.h"

+#include "settingsdialogproton.h"

+#include "settingsdialogpython.h"

+#include "settingsdialogtheme.h"

+#include "settingsdialogworkarounds.h"

 #include "ui_settingsdialog.h"

 

 using namespace MOBase;

@@ -46,14 +47,16 @@ SettingsDialog::SettingsDialog(PluginContainer* pluginContainer, Settings& setti
   m_tabs.push_back(std::unique_ptr<SettingsTab>(new PathsSettingsTab(settings, *this)));

   m_tabs.push_back(

       std::unique_ptr<SettingsTab>(new DiagnosticsSettingsTab(settings, *this)));

-  m_tabs.push_back(std::unique_ptr<SettingsTab>(new NexusSettingsTab(settings, *this)));
-  m_tabs.push_back(std::unique_ptr<SettingsTab>(
-      new PluginsSettingsTab(settings, m_pluginContainer, *this)));
-  m_tabs.push_back(
-      std::unique_ptr<SettingsTab>(new ProtonSettingsTab(settings, *this)));
-  m_tabs.push_back(
-      std::unique_ptr<SettingsTab>(new WorkaroundsSettingsTab(settings, *this)));
-}
+  m_tabs.push_back(std::unique_ptr<SettingsTab>(new NexusSettingsTab(settings, *this)));

+  m_tabs.push_back(std::unique_ptr<SettingsTab>(

+      new PluginsSettingsTab(settings, m_pluginContainer, *this)));

+  m_tabs.push_back(

+      std::unique_ptr<SettingsTab>(new ProtonSettingsTab(settings, *this)));

+  m_tabs.push_back(

+      std::unique_ptr<SettingsTab>(new PythonSettingsTab(settings, *this)));

+  m_tabs.push_back(

+      std::unique_ptr<SettingsTab>(new WorkaroundsSettingsTab(settings, *this)));

+}

 

 PluginContainer* SettingsDialog::pluginContainer()

 {

diff --git a/src/src/settingsdialog.ui b/src/src/settingsdialog.ui
index 646b9b6..2089c06 100644
--- a/src/src/settingsdialog.ui
+++ b/src/src/settingsdialog.ui
@@ -1897,6 +1897,167 @@ If you disable this feature, MO will only display official DLCs this way. Please
        </item>
       </layout>
      </widget>
+     <widget class="QWidget" name="pythonTab">
+      <attribute name="title">
+       <string>Python</string>
+      </attribute>
+      <layout class="QVBoxLayout" name="verticalLayout_python">
+       <item>
+        <widget class="QGroupBox" name="groupBox_python">
+         <property name="title">
+          <string>Python Plugin Support</string>
+         </property>
+         <layout class="QGridLayout" name="gridLayout_python">
+          <item row="0" column="0">
+           <widget class="QLabel" name="pythonEnableLabel">
+            <property name="text">
+             <string>Enable Python Plugins:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="0" column="1" colspan="2">
+           <widget class="QCheckBox" name="pythonEnableCheck">
+            <property name="text">
+             <string>Load .py plugins (requires Python 3 and PyQt6)</string>
+            </property>
+           </widget>
+          </item>
+          <item row="1" column="0">
+           <widget class="QLabel" name="pythonPathLabel">
+            <property name="text">
+             <string>Python Path:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="1" column="1">
+           <widget class="QLineEdit" name="pythonPathEdit">
+            <property name="readOnly">
+             <bool>true</bool>
+            </property>
+            <property name="placeholderText">
+             <string>Auto-detected</string>
+            </property>
+           </widget>
+          </item>
+          <item row="1" column="2">
+           <widget class="QPushButton" name="pythonRefreshButton">
+            <property name="text">
+             <string>Detect</string>
+            </property>
+           </widget>
+          </item>
+          <item row="2" column="0">
+           <widget class="QLabel" name="pythonVersionLabel">
+            <property name="text">
+             <string>Version:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="2" column="1" colspan="2">
+           <widget class="QLabel" name="pythonVersionValue">
+            <property name="text">
+             <string>Not detected</string>
+            </property>
+           </widget>
+          </item>
+         </layout>
+        </widget>
+       </item>
+       <item>
+        <widget class="QGroupBox" name="groupBox_venv">
+         <property name="title">
+          <string>Virtual Environment</string>
+         </property>
+         <layout class="QGridLayout" name="gridLayout_venv">
+          <item row="0" column="0">
+           <widget class="QLabel" name="venvPathLabel">
+            <property name="text">
+             <string>Venv Location:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="0" column="1" colspan="2">
+           <widget class="QLineEdit" name="venvPathEdit">
+            <property name="readOnly">
+             <bool>true</bool>
+            </property>
+           </widget>
+          </item>
+          <item row="1" column="0">
+           <widget class="QLabel" name="venvStatusLabel">
+            <property name="text">
+             <string>Status:</string>
+            </property>
+           </widget>
+          </item>
+          <item row="1" column="1" colspan="2">
+           <widget class="QLabel" name="venvStatusValue">
+            <property name="text">
+             <string>Not created</string>
+            </property>
+           </widget>
+          </item>
+          <item row="2" column="0">
+           <widget class="QPushButton" name="createVenvButton">
+            <property name="text">
+             <string>Create Virtual Environment</string>
+            </property>
+            <property name="toolTip">
+             <string>Creates a Python virtual environment and installs PyQt6. Required for loading .py plugins.</string>
+            </property>
+           </widget>
+          </item>
+          <item row="2" column="1">
+           <widget class="QPushButton" name="deleteVenvButton">
+            <property name="text">
+             <string>Delete Venv</string>
+            </property>
+           </widget>
+          </item>
+          <item row="2" column="2">
+           <widget class="QPushButton" name="openVenvFolderButton">
+            <property name="text">
+             <string>Open Folder</string>
+            </property>
+           </widget>
+          </item>
+          <item row="3" column="0" colspan="3">
+           <widget class="QTextEdit" name="pythonLogOutput">
+            <property name="readOnly">
+             <bool>true</bool>
+            </property>
+            <property name="visible">
+             <bool>false</bool>
+            </property>
+            <property name="maximumHeight">
+             <number>150</number>
+            </property>
+            <property name="font">
+             <font>
+              <family>monospace</family>
+              <pointsize>9</pointsize>
+             </font>
+            </property>
+           </widget>
+          </item>
+         </layout>
+        </widget>
+       </item>
+       <item>
+        <spacer name="verticalSpacer_python">
+         <property name="orientation">
+          <enum>Qt::Vertical</enum>
+         </property>
+         <property name="sizeHint" stdset="0">
+          <size>
+           <width>20</width>
+           <height>40</height>
+          </size>
+         </property>
+        </spacer>
+       </item>
+      </layout>
+     </widget>
      <widget class="QWidget" name="workaroundTab">
       <attribute name="title">
        <string>Workarounds</string>
diff --git a/src/src/settingsdialogpython.cpp b/src/src/settingsdialogpython.cpp
new file mode 100644
index 0000000..ebad6eb
--- /dev/null
+++ b/src/src/settingsdialogpython.cpp
@@ -0,0 +1,206 @@
+#include "settingsdialogpython.h"
+
+#include "fluorinepaths.h"
+#include "ui_settingsdialog.h"
+
+#include <log.h>
+#include <uibase/utility.h>
+
+#include <QCheckBox>
+#include <QDir>
+#include <QFileInfo>
+#include <QMessageBox>
+#include <QProcess>
+#include <QPushButton>
+#include <QSettings>
+#include <QStandardPaths>
+
+PythonSettingsTab::PythonSettingsTab(Settings& s, SettingsDialog& d)
+    : QObject(&d), SettingsTab(s, d)
+{
+  m_venvPath = fluorineDataDir() + "/python-venv";
+  ui->venvPathEdit->setText(m_venvPath);
+
+  // Load saved state
+  bool pythonEnabled = QSettings().value("fluorine/python_enabled", false).toBool();
+  ui->pythonEnableCheck->setChecked(pythonEnabled);
+
+  detectPython();
+  refreshVenvState();
+
+  QObject::connect(ui->pythonRefreshButton, &QPushButton::clicked, this,
+                   &PythonSettingsTab::detectPython);
+  QObject::connect(ui->createVenvButton, &QPushButton::clicked, this,
+                   &PythonSettingsTab::onCreateVenv);
+  QObject::connect(ui->deleteVenvButton, &QPushButton::clicked, this,
+                   &PythonSettingsTab::onDeleteVenv);
+  QObject::connect(ui->openVenvFolderButton, &QPushButton::clicked, this,
+                   &PythonSettingsTab::onOpenVenvFolder);
+}
+
+void PythonSettingsTab::update()
+{
+  QSettings().setValue("fluorine/python_enabled",
+                       ui->pythonEnableCheck->isChecked());
+}
+
+void PythonSettingsTab::detectPython()
+{
+  m_pythonPath = QStandardPaths::findExecutable("python3");
+  if (m_pythonPath.isEmpty()) {
+    m_pythonPath = QStandardPaths::findExecutable("python");
+  }
+
+  if (m_pythonPath.isEmpty()) {
+    ui->pythonPathEdit->setText("");
+    ui->pythonVersionValue->setText("Python 3 not found in PATH");
+    return;
+  }
+
+  ui->pythonPathEdit->setText(m_pythonPath);
+
+  // Get version
+  QProcess proc;
+  proc.start(m_pythonPath, {"--version"});
+  proc.waitForFinished(5000);
+
+  if (proc.exitCode() == 0) {
+    QString version = QString::fromUtf8(proc.readAllStandardOutput()).trimmed();
+    if (version.isEmpty()) {
+      version = QString::fromUtf8(proc.readAllStandardError()).trimmed();
+    }
+    ui->pythonVersionValue->setText(version);
+  } else {
+    ui->pythonVersionValue->setText("Error detecting version");
+  }
+}
+
+void PythonSettingsTab::refreshVenvState()
+{
+  QDir venvDir(m_venvPath);
+  bool exists = venvDir.exists() && venvDir.exists("bin/python3");
+
+  if (exists) {
+    // Check if PyQt6 is installed
+    QProcess proc;
+    proc.start(m_venvPath + "/bin/python3",
+               {"-c", "import PyQt6; print(PyQt6.__file__)"});
+    proc.waitForFinished(5000);
+
+    if (proc.exitCode() == 0) {
+      ui->venvStatusValue->setText("Active (PyQt6 installed)");
+    } else {
+      ui->venvStatusValue->setText("Active (PyQt6 NOT installed)");
+    }
+  } else {
+    ui->venvStatusValue->setText("Not created");
+  }
+
+  ui->deleteVenvButton->setEnabled(exists);
+  ui->openVenvFolderButton->setEnabled(exists);
+}
+
+void PythonSettingsTab::onCreateVenv()
+{
+  if (m_pythonPath.isEmpty()) {
+    QMessageBox::warning(parentWidget(), tr("No Python"),
+                         tr("Python 3 was not found in PATH.\n\n"
+                            "Install Python 3 using your package manager:\n"
+                            "  Arch: pacman -S python\n"
+                            "  Ubuntu: apt install python3 python3-venv\n"
+                            "  Fedora: dnf install python3"));
+    return;
+  }
+
+  ui->pythonLogOutput->setVisible(true);
+  ui->pythonLogOutput->clear();
+  ui->venvStatusValue->setText("Creating virtual environment...");
+
+  // Create venv
+  {
+    QProcess proc;
+    proc.start(m_pythonPath, {"-m", "venv", m_venvPath});
+    proc.waitForFinished(30000);
+
+    QString output = QString::fromUtf8(proc.readAllStandardOutput());
+    QString errors = QString::fromUtf8(proc.readAllStandardError());
+    if (!output.isEmpty())
+      ui->pythonLogOutput->append(output);
+    if (!errors.isEmpty())
+      ui->pythonLogOutput->append(errors);
+
+    if (proc.exitCode() != 0) {
+      ui->venvStatusValue->setText("Failed to create venv");
+      ui->pythonLogOutput->append("venv creation failed with exit code " +
+                                  QString::number(proc.exitCode()));
+      return;
+    }
+  }
+
+  ui->pythonLogOutput->append("Virtual environment created. Installing PyQt6...");
+  ui->venvStatusValue->setText("Installing PyQt6...");
+
+  // Install PyQt6
+  {
+    QProcess proc;
+    proc.start(m_venvPath + "/bin/pip",
+               {"install", "--upgrade", "pip", "PyQt6"});
+    proc.waitForFinished(120000);  // PyQt6 is large, give it time
+
+    QString output = QString::fromUtf8(proc.readAllStandardOutput());
+    QString errors = QString::fromUtf8(proc.readAllStandardError());
+    if (!output.isEmpty())
+      ui->pythonLogOutput->append(output);
+    if (!errors.isEmpty())
+      ui->pythonLogOutput->append(errors);
+
+    if (proc.exitCode() != 0) {
+      ui->venvStatusValue->setText("PyQt6 installation failed");
+      ui->pythonLogOutput->append("pip install failed with exit code " +
+                                  QString::number(proc.exitCode()));
+      refreshVenvState();
+      return;
+    }
+  }
+
+  ui->pythonLogOutput->append("PyQt6 installed successfully.");
+  MOBase::log::info("Python venv created at {}", m_venvPath);
+
+  refreshVenvState();
+}
+
+void PythonSettingsTab::onDeleteVenv()
+{
+  QDir venvDir(m_venvPath);
+  if (!venvDir.exists()) {
+    refreshVenvState();
+    return;
+  }
+
+  auto result = QMessageBox::question(
+      parentWidget(), tr("Delete Virtual Environment"),
+      tr("Delete the Python virtual environment at:\n%1\n\n"
+         "This will disable .py plugin loading until recreated.")
+          .arg(m_venvPath));
+
+  if (result != QMessageBox::Yes)
+    return;
+
+  if (venvDir.removeRecursively()) {
+    ui->pythonLogOutput->setVisible(false);
+    MOBase::log::info("Python venv deleted at {}", m_venvPath);
+  } else {
+    QMessageBox::warning(parentWidget(), tr("Error"),
+                         tr("Failed to delete the virtual environment."));
+  }
+
+  refreshVenvState();
+}
+
+void PythonSettingsTab::onOpenVenvFolder()
+{
+  QDir venvDir(m_venvPath);
+  if (venvDir.exists()) {
+    MOBase::shell::Explore(venvDir);
+  }
+}
diff --git a/src/src/settingsdialogpython.h b/src/src/settingsdialogpython.h
new file mode 100644
index 0000000..187d04b
--- /dev/null
+++ b/src/src/settingsdialogpython.h
@@ -0,0 +1,29 @@
+#ifndef SETTINGSDIALOGPYTHON_H
+#define SETTINGSDIALOGPYTHON_H
+
+#include <QObject>
+
+#include "settings.h"
+#include "settingsdialog.h"
+
+class PythonSettingsTab : public QObject, public SettingsTab
+{
+  Q_OBJECT
+
+public:
+  PythonSettingsTab(Settings& settings, SettingsDialog& dialog);
+
+  void update() override;
+
+private:
+  void detectPython();
+  void refreshVenvState();
+  void onCreateVenv();
+  void onDeleteVenv();
+  void onOpenVenvFolder();
+
+  QString m_pythonPath;
+  QString m_venvPath;
+};
+
+#endif  // SETTINGSDIALOGPYTHON_H
diff --git a/src/src/vfs/mo2filesystem.cpp b/src/src/vfs/mo2filesystem.cpp
index 2b1ef5f..22116f0 100644
--- a/src/src/vfs/mo2filesystem.cpp
+++ b/src/src/vfs/mo2filesystem.cpp
@@ -28,7 +28,8 @@ constexpr double ATTR_CACHE_SECONDS   = 86400.0;
 void fillStatForDir(struct stat* st, fuse_ino_t ino, uid_t uid, gid_t gid);
 void fillStatForFile(struct stat* st, fuse_ino_t ino, uid_t uid, gid_t gid,
                      uint64_t size,
-                     const std::chrono::system_clock::time_point& mtime);
+                     const std::chrono::system_clock::time_point& mtime,
+                     const std::string& real_path = {});
 
 void maybeLogCounters(Mo2FsContext* ctx)
 {
@@ -209,6 +210,7 @@ struct ChildSnapshot
   bool is_dir = false;
   uint64_t size = 0;
   std::chrono::system_clock::time_point mtime{};
+  std::string real_path;
 };
 
 std::vector<ChildSnapshot> listChildrenSnapshot(
@@ -229,8 +231,9 @@ std::vector<ChildSnapshot> listChildrenSnapshot(
     snap.name   = name;
     snap.is_dir = child->is_directory;
     if (!child->is_directory) {
-      snap.size  = child->file_info.size;
-      snap.mtime = child->file_info.mtime;
+      snap.size      = child->file_info.size;
+      snap.mtime     = child->file_info.mtime;
+      snap.real_path = child->file_info.real_path;
     }
     out.push_back(std::move(snap));
   }
@@ -256,7 +259,8 @@ std::vector<Mo2FsContext::DirEntry> buildDirEntries(
     const std::string childPath = joinPath(path, child.name);
     entries.push_back(
         Mo2FsContext::DirEntry{ctx->inodes->getOrCreate(childPath), child.name,
-                               child.is_dir, child.size, child.mtime});
+                               child.is_dir, child.size, child.mtime,
+                               child.real_path});
   }
 
   return entries;
@@ -329,8 +333,20 @@ std::vector<char> buildReaddirBlob(
   for (const auto& entry : entries) {
     struct stat st;
     std::memset(&st, 0, sizeof(st));
-    st.st_ino  = entry.ino;
-    st.st_mode = entry.is_dir ? (S_IFDIR | 0755) : (S_IFREG | 0644);
+    st.st_ino = entry.ino;
+    if (entry.is_dir) {
+      st.st_mode = S_IFDIR | 0755;
+    } else {
+      // Preserve executable bits from the real file on disk.
+      mode_t mode = 0644;
+      if (!entry.real_path.empty()) {
+        struct stat real_st;
+        if (::stat(entry.real_path.c_str(), &real_st) == 0) {
+          mode = real_st.st_mode & 0777;
+        }
+      }
+      st.st_mode = S_IFREG | mode;
+    }
 
     const size_t entSize =
         fuse_add_direntry(req, nullptr, 0, entry.name.c_str(), &st, 0);
@@ -362,7 +378,7 @@ std::vector<char> buildReaddirPlusBlob(
       fillStatForDir(&e.attr, entry.ino, ctx->uid, ctx->gid);
     } else {
       fillStatForFile(&e.attr, entry.ino, ctx->uid, ctx->gid, entry.size,
-                      entry.mtime);
+                      entry.mtime, entry.real_path);
     }
 
     const size_t entSize =
@@ -444,16 +460,27 @@ void fillStatForDir(struct stat* st, fuse_ino_t ino, uid_t uid, gid_t gid)
 
 void fillStatForFile(struct stat* st, fuse_ino_t ino, uid_t uid, gid_t gid,
                      uint64_t size,
-                     const std::chrono::system_clock::time_point& mtime)
+                     const std::chrono::system_clock::time_point& mtime,
+                     const std::string& real_path = {})
 {
   std::memset(st, 0, sizeof(struct stat));
   st->st_ino   = ino;
-  st->st_mode  = S_IFREG | 0644;
   st->st_nlink = 1;
   st->st_uid   = uid;
   st->st_gid   = gid;
   st->st_size  = static_cast<off_t>(size);
 
+  // Preserve executable bits from the real file on disk so native Linux
+  // executables added as mods can actually be launched through the VFS.
+  mode_t mode = 0644;
+  if (!real_path.empty()) {
+    struct stat real_st;
+    if (::stat(real_path.c_str(), &real_st) == 0) {
+      mode = real_st.st_mode & 0777;
+    }
+  }
+  st->st_mode = S_IFREG | mode;
+
   const auto secs = std::chrono::duration_cast<std::chrono::seconds>(
       mtime.time_since_epoch());
   st->st_mtim.tv_sec = secs.count();
@@ -473,7 +500,8 @@ void replyEntryFromSnapshot(fuse_req_t req, const Mo2FsContext* ctx, fuse_ino_t
   if (snap.is_directory) {
     fillStatForDir(&e.attr, ino, ctx->uid, ctx->gid);
   } else {
-    fillStatForFile(&e.attr, ino, ctx->uid, ctx->gid, snap.size, snap.mtime);
+    fillStatForFile(&e.attr, ino, ctx->uid, ctx->gid, snap.size, snap.mtime,
+                    snap.real_path);
   }
 
   fuse_reply_entry(req, &e);
@@ -683,7 +711,8 @@ void mo2_getattr(fuse_req_t req, fuse_ino_t ino, struct fuse_file_info* /*fi*/)
   if (snap.is_directory) {
     fillStatForDir(&st, ino, ctx->uid, ctx->gid);
   } else {
-    fillStatForFile(&st, ino, ctx->uid, ctx->gid, snap.size, snap.mtime);
+    fillStatForFile(&st, ino, ctx->uid, ctx->gid, snap.size, snap.mtime,
+                    snap.real_path);
   }
 
   {
@@ -800,8 +829,19 @@ void mo2_readdir(fuse_req_t req, fuse_ino_t ino, size_t size, off_t off,
   for (size_t i = static_cast<size_t>(off); i < entries->size(); ++i) {
     struct stat st;
     std::memset(&st, 0, sizeof(st));
-    st.st_ino  = (*entries)[i].ino;
-    st.st_mode = (*entries)[i].is_dir ? (S_IFDIR | 0755) : (S_IFREG | 0644);
+    st.st_ino = (*entries)[i].ino;
+    if ((*entries)[i].is_dir) {
+      st.st_mode = S_IFDIR | 0755;
+    } else {
+      mode_t mode = 0644;
+      if (!(*entries)[i].real_path.empty()) {
+        struct stat real_st;
+        if (::stat((*entries)[i].real_path.c_str(), &real_st) == 0) {
+          mode = real_st.st_mode & 0777;
+        }
+      }
+      st.st_mode = S_IFREG | mode;
+    }
 
     const size_t ent = fuse_add_direntry(req, buf.data() + used, size - used,
                                          (*entries)[i].name.c_str(), &st,
@@ -1164,7 +1204,7 @@ void mo2_write(fuse_req_t req, fuse_ino_t /*ino*/, const char* buf, size_t size,
   fuse_reply_write(req, static_cast<size_t>(written));
 }
 
-void mo2_create(fuse_req_t req, fuse_ino_t parent, const char* name, mode_t /*mode*/,
+void mo2_create(fuse_req_t req, fuse_ino_t parent, const char* name, mode_t mode,
                 struct fuse_file_info* fi)
 {
   Mo2FsContext* ctx = getContext(req);
@@ -1196,7 +1236,8 @@ void mo2_create(fuse_req_t req, fuse_ino_t parent, const char* name, mode_t /*mo
     std::error_code ec;
     fs::create_directories(fs::path(realPath).parent_path(), ec);
     // Create the file
-    int tmpFd = open(realPath.c_str(), O_WRONLY | O_CREAT | O_TRUNC, 0644);
+    int tmpFd = open(realPath.c_str(), O_WRONLY | O_CREAT | O_TRUNC,
+                     mode != 0 ? (mode & 07777) : 0644);
     if (tmpFd < 0) {
       // Fall back to staging
       trackedMod.clear();
@@ -1259,7 +1300,8 @@ void mo2_create(fuse_req_t req, fuse_ino_t parent, const char* name, mode_t /*mo
   e.ino           = newIno;
   e.attr_timeout  = TTL_SECONDS;
   e.entry_timeout = TTL_SECONDS;
-  fillStatForFile(&e.attr, newIno, ctx->uid, ctx->gid, snap.size, snap.mtime);
+  fillStatForFile(&e.attr, newIno, ctx->uid, ctx->gid, snap.size, snap.mtime,
+                  snap.real_path);
 
   fuse_reply_create(req, &e, fi);
 }
@@ -1447,6 +1489,14 @@ void mo2_setattr(fuse_req_t req, fuse_ino_t ino, struct stat* attr, int to_set,
     updateFileNode(ctx, path, target, targetIsTracked ? "Mod" : "Staging");
   }
 
+  // Handle chmod — propagate permission changes to the real file on disk.
+  if ((to_set & FUSE_SET_ATTR_MODE) != 0 && attr != nullptr) {
+    const auto snap = snapshotForPath(ctx, path);
+    if (snap.found && !snap.is_directory && !snap.real_path.empty()) {
+      ::chmod(snap.real_path.c_str(), attr->st_mode & 07777);
+    }
+  }
+
   // Handle explicit timestamp changes (utimensat / Wine SetFileTime)
   if ((to_set & (FUSE_SET_ATTR_MTIME | FUSE_SET_ATTR_MTIME_NOW |
                  FUSE_SET_ATTR_ATIME | FUSE_SET_ATTR_ATIME_NOW)) != 0 &&
@@ -1523,7 +1573,8 @@ void mo2_setattr(fuse_req_t req, fuse_ino_t ino, struct stat* attr, int to_set,
   if (snap.is_directory) {
     fillStatForDir(&st, ino, ctx->uid, ctx->gid);
   } else {
-    fillStatForFile(&st, ino, ctx->uid, ctx->gid, snap.size, snap.mtime);
+    fillStatForFile(&st, ino, ctx->uid, ctx->gid, snap.size, snap.mtime,
+                    snap.real_path);
   }
   fuse_reply_attr(req, &st, TTL_SECONDS);
 }
diff --git a/src/src/vfs/mo2filesystem.h b/src/src/vfs/mo2filesystem.h
index 3877bbb..40e0ed7 100644
--- a/src/src/vfs/mo2filesystem.h
+++ b/src/src/vfs/mo2filesystem.h
@@ -51,6 +51,7 @@ struct Mo2FsContext
     bool is_dir = false;
     uint64_t size = 0;
     std::chrono::system_clock::time_point mtime{};
+    std::string real_path;
   };
   struct OpenDir
   {