Fluorine Manager: full Linux port of Mod Organizer 2

Complete native Linux port with FUSE-based virtual filesystem,
Proton/umu-run integration, and Flatpak packaging.

Key features:
- FUSE VFS replacing Windows USVFS (in-process + standalone helper for Flatpak)
- Proton/GE-Proton/umu-run launcher with env var forwarding
- Flatpak support (sandbox-aware VFS, NXM handler, umu-run)
- Wine prefix management UI
- Case-insensitive path resolution for Linux filesystems
- QSettings-safe INI handling (avoids Bethesda INI corruption)
- Portable instance support with auto-generated launcher scripts

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

11 files changed, 590 insertions, 0 deletions

diff --git a/libs/check_fnis/.clang-format b/libs/check_fnis/.clang-format
new file mode 100644
index 0000000..6098e1f
--- /dev/null
+++ b/libs/check_fnis/.clang-format
@@ -0,0 +1,41 @@
+---
+# We'll use defaults from the LLVM style, but with 4 columns indentation.
+BasedOnStyle: LLVM
+IndentWidth: 2
+---
+Language: Cpp
+DeriveLineEnding: false
+UseCRLF: true
+DerivePointerAlignment: false
+PointerAlignment: Left
+AlignConsecutiveAssignments: true
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLambdasOnASingleLine: Empty
+AlwaysBreakTemplateDeclarations: Yes
+AccessModifierOffset: -2
+AlignTrailingComments: true
+SpacesBeforeTrailingComments: 2
+NamespaceIndentation: Inner
+MaxEmptyLinesToKeep: 1
+BreakBeforeBraces: Custom
+BraceWrapping:
+  AfterCaseLabel: false
+  AfterClass: true
+  AfterControlStatement: false
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: true
+  AfterStruct: true
+  AfterUnion: true
+  AfterExternBlock: true
+  BeforeCatch: false
+  BeforeElse: false
+  BeforeLambdaBody: false
+  BeforeWhile: false
+  IndentBraces: false
+  SplitEmptyFunction: false
+  SplitEmptyRecord: false
+  SplitEmptyNamespace: true
+ColumnLimit: 88
+ForEachMacros: ['Q_FOREACH', 'foreach']
diff --git a/libs/check_fnis/.gitattributes b/libs/check_fnis/.gitattributes
new file mode 100644
index 0000000..f869712
--- /dev/null
+++ b/libs/check_fnis/.gitattributes
@@ -0,0 +1,7 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+* text=auto
+
+# Explicitly declare text files you want to always be normalized and converted
+# to native line endings on checkout.
+*.cpp text eol=crlf
+*.h text eol=crlf
diff --git a/libs/check_fnis/.gitignore b/libs/check_fnis/.gitignore
new file mode 100644
index 0000000..cf71be7
--- /dev/null
+++ b/libs/check_fnis/.gitignore
@@ -0,0 +1,5 @@
+edit
+CMakeLists.txt.user
+/msbuild.log
+/*std*.log
+/*build
diff --git a/libs/check_fnis/.pre-commit-config.yaml b/libs/check_fnis/.pre-commit-config.yaml
new file mode 100644
index 0000000..eb8969c
--- /dev/null
+++ b/libs/check_fnis/.pre-commit-config.yaml
@@ -0,0 +1,20 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-merge-conflict
+      - id: check-case-conflict
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v21.1.8
+    hooks:
+    - id: clang-format
+      'types_or': [c++, c]
+
+ci:
+  autofix_commit_msg: "[pre-commit.ci] Auto fixes from pre-commit.com hooks."
+  autofix_prs: true
+  autoupdate_commit_msg: "[pre-commit.ci] Pre-commit autoupdate."
+  autoupdate_schedule: quarterly
+  submodules: false
diff --git a/libs/check_fnis/CMakeLists.txt b/libs/check_fnis/CMakeLists.txt
new file mode 100644
index 0000000..f7eb6af
--- /dev/null
+++ b/libs/check_fnis/CMakeLists.txt
@@ -0,0 +1,5 @@
+cmake_minimum_required(VERSION 3.16)
+
+project(check_fnis)
+
+add_subdirectory(src)
diff --git a/libs/check_fnis/CMakePresets.json b/libs/check_fnis/CMakePresets.json
new file mode 100644
index 0000000..cc009b3
--- /dev/null
+++ b/libs/check_fnis/CMakePresets.json
@@ -0,0 +1,57 @@
+{
+  "configurePresets": [
+    {
+      "errors": {
+        "deprecated": true
+      },
+      "hidden": true,
+      "name": "cmake-dev",
+      "warnings": {
+        "deprecated": true,
+        "dev": true
+      }
+    },
+    {
+      "cacheVariables": {
+        "VCPKG_MANIFEST_NO_DEFAULT_FEATURES": {
+          "type": "BOOL",
+          "value": "ON"
+        }
+      },
+      "toolchainFile": "$env{VCPKG_ROOT}/scripts/buildsystems/vcpkg.cmake",
+      "hidden": true,
+      "name": "vcpkg"
+    },
+    {
+      "hidden": true,
+      "inherits": ["vcpkg"],
+      "name": "vcpkg-dev"
+    },
+    {
+      "binaryDir": "${sourceDir}/vsbuild",
+      "architecture": {
+        "strategy": "set",
+        "value": "x64"
+      },
+      "cacheVariables": {
+        "CMAKE_CXX_FLAGS": "/EHsc /MP /W4",
+        "VCPKG_TARGET_TRIPLET": {
+          "type": "STRING",
+          "value": "x64-windows-static-md"
+        }
+      },
+      "generator": "Visual Studio 17 2022",
+      "inherits": ["cmake-dev", "vcpkg-dev"],
+      "name": "vs2022-windows",
+      "toolset": "v143"
+    }
+  ],
+  "buildPresets": [
+    {
+      "name": "vs2022-windows",
+      "resolvePackageReferences": "on",
+      "configurePreset": "vs2022-windows"
+    }
+  ],
+  "version": 4
+}
diff --git a/libs/check_fnis/src/CMakeLists.txt b/libs/check_fnis/src/CMakeLists.txt
new file mode 100644
index 0000000..38451b1
--- /dev/null
+++ b/libs/check_fnis/src/CMakeLists.txt
@@ -0,0 +1,14 @@
+cmake_minimum_required(VERSION 3.16)
+
+file(GLOB check_fnis_SOURCES CONFIGURE_DEPENDS
+  ${CMAKE_CURRENT_SOURCE_DIR}/*.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/*.h
+  ${CMAKE_CURRENT_SOURCE_DIR}/*.ui
+  ${CMAKE_CURRENT_SOURCE_DIR}/*.qrc
+)
+
+add_library(check_fnis SHARED ${check_fnis_SOURCES})
+mo2_configure_plugin(check_fnis NO_SOURCES WARNINGS OFF)
+target_link_libraries(check_fnis PRIVATE mo2::uibase)
+
+mo2_install_plugin(check_fnis)
diff --git a/libs/check_fnis/src/check_fnis_en.ts b/libs/check_fnis/src/check_fnis_en.ts
new file mode 100644
index 0000000..408428e
--- /dev/null
+++ b/libs/check_fnis/src/check_fnis_en.ts
@@ -0,0 +1,66 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE TS>
+<TS version="2.1" language="en_US">
+<context>
+    <name>CheckFNIS</name>
+    <message>
+        <location filename="checkfnis.cpp" line="74"/>
+        <source>FNIS Checker</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="84"/>
+        <source>Checks if FNIS behaviours need to be updated whenever you start the game. This is only relevant for Skyrim and if FNIS is installed.&lt;br&gt;</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="218"/>
+        <source>Run FNIS before %1?</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="219"/>
+        <source>FNIS source data has been changed. You should run GenerateFNIS.exe now.</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="226"/>
+        <source>Failed to start %1</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="232"/>
+        <location filename="checkfnis.cpp" line="239"/>
+        <location filename="checkfnis.cpp" line="263"/>
+        <source>Start %1?</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="233"/>
+        <source>FNIS reported a %1, do you want to run the application anyway?</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="234"/>
+        <location filename="checkfnis.cpp" line="265"/>
+        <source>warning</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="235"/>
+        <location filename="checkfnis.cpp" line="266"/>
+        <source>critical error</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="240"/>
+        <source>Failed to determine FNIS exit code, do you want to run the application anyway?</source>
+        <translation type="unfinished"></translation>
+    </message>
+    <message>
+        <location filename="checkfnis.cpp" line="264"/>
+        <source>FNIS reported a %1. Do you want to assume it worked?</source>
+        <translation type="unfinished"></translation>
+    </message>
+</context>
+</TS>
diff --git a/libs/check_fnis/src/checkfnis.cpp b/libs/check_fnis/src/checkfnis.cpp
new file mode 100644
index 0000000..73f2ac0
--- /dev/null
+++ b/libs/check_fnis/src/checkfnis.cpp
@@ -0,0 +1,293 @@
+#include "checkfnis.h"
+
+#include <uibase/iplugingame.h>
+#include <uibase/pluginsetting.h>
+#include <uibase/questionboxmemory.h>
+#include <uibase/report.h>
+#include <uibase/scopeguard.h>
+
+#include <QCryptographicHash>
+#include <QDialogButtonBox>
+#include <QDir>
+#include <QFile>
+#include <QFileInfo>
+#include <QMessageBox>
+#include <QStringList>
+#include <QVariant>
+
+#include <Qt>       // for Qt::CaseInsensitive
+#include <QtDebug>  // for qCritical, qDebug
+
+#include <functional>
+
+using namespace MOBase;
+
+CheckFNIS::CheckFNIS()
+    : m_MOInfo(nullptr), m_Active(false),
+      m_MatchExpressions(std::vector<QRegularExpression>{
+          // MSVC2013 bug. The (std::vector<QRegExp> shouldn't be necessary
+          QRegularExpression("\\\\FNIS_.*_List\\.txt$",
+                             QRegularExpression::PatternOption::CaseInsensitiveOption),
+          QRegularExpression("\\\\FNIS.*Behavior\\.txt$",
+                             QRegularExpression::PatternOption::CaseInsensitiveOption),
+          QRegularExpression("\\\\PatchList\\.txt$",
+                             QRegularExpression::PatternOption::CaseInsensitiveOption),
+          QRegularExpression(
+              "\\\\skeleton.*\\.hkx$",
+              QRegularExpression::PatternOption::CaseInsensitiveOption)}),
+      m_SensitiveMatchExpressions(std::vector<QRegularExpression>{
+          QRegularExpression("\\\\animations\\\\.*\\.hkx$",
+                             QRegularExpression::PatternOption::CaseInsensitiveOption)})
+{}
+
+CheckFNIS::~CheckFNIS() {}
+
+bool CheckFNIS::init(IOrganizer* moInfo)
+{
+  m_MOInfo = moInfo;
+
+  if (!moInfo->onAboutToRun([this](const auto& binary) {
+        return fnisCheck(binary);
+      })) {
+    qCritical("failed to connect to about to run event");
+    return false;
+  }
+
+  if (!moInfo->onFinishedRun(std::bind(&CheckFNIS::fnisEndCheck, this,
+                                       std::placeholders::_1, std::placeholders::_2))) {
+    qCritical("failed to connect to finished run event");
+    return false;
+  }
+
+  return true;
+}
+
+QString CheckFNIS::name() const
+{
+  return "FNIS Checker";
+}
+
+QString CheckFNIS::localizedName() const
+{
+  return tr("FNIS Checker");
+}
+
+QString CheckFNIS::author() const
+{
+  return "Tannin";
+}
+
+QString CheckFNIS::description() const
+{
+  return tr("Checks if FNIS behaviours need to be updated whenever you start the game."
+            " This is only relevant for Skyrim and if FNIS is installed.<br>");
+}
+
+VersionInfo CheckFNIS::version() const
+{
+  return VersionInfo(1, 0, 1, VersionInfo::RELEASE_FINAL);
+}
+
+std::vector<std::shared_ptr<const MOBase::IPluginRequirement>>
+CheckFNIS::requirements() const
+{
+  return {Requirements::gameDependency("Skyrim")};
+}
+
+QList<PluginSetting> CheckFNIS::settings() const
+{
+  QList<PluginSetting> result;
+  result.push_back(PluginSetting("sensitive",
+                                 "check changes on non-fnis animations. Makes this "
+                                 "more reliable but will cause FNIS to be called more "
+                                 "often than necessary.",
+                                 QVariant(false)));
+  return result;
+}
+
+bool CheckFNIS::testFileRelevant(const IOrganizer::FileInfo& fileName) const
+{
+  if (!fileName.archive.isEmpty()) {
+    return false;
+  }
+
+  for (auto& expr : m_MatchExpressions) {
+    auto match = expr.match(fileName.filePath);
+    if (match.hasMatch()) {
+      return true;
+    }
+  }
+
+  if (m_MOInfo->pluginSetting(name(), "sensitive").toBool()) {
+    for (auto& expr : m_SensitiveMatchExpressions) {
+      auto match = expr.match(fileName.filePath);
+      if (match.hasMatch()) {
+        return true;
+      }
+    }
+  }
+
+  return false;
+}
+
+void CheckFNIS::findRelevantFilesRecursive(const QString& path,
+                                           QMap<QString, QString>& fileList) const
+{
+  // find all relevant files
+  QList<IOrganizer::FileInfo> files = m_MOInfo->findFileInfos(
+      path, std::bind(&CheckFNIS::testFileRelevant, this, std::placeholders::_1));
+  foreach (const IOrganizer::FileInfo& fileInfo, files) {
+    QFile file(fileInfo.filePath);
+    if (file.open(QIODevice::ReadOnly)) {
+      QString hash(
+          QCryptographicHash::hash(file.readAll(), QCryptographicHash::Md5).toHex());
+      fileList.insert(fileInfo.filePath, hash);
+    } else {
+      qCritical("failed to open %s", qUtf8Printable(fileInfo.filePath));
+    }
+  }
+
+  QStringList subDirectories = m_MOInfo->listDirectories(path);
+  foreach (const QString& directory, subDirectories) {
+    findRelevantFilesRecursive(QDir(path).filePath(directory), fileList);
+  }
+}
+
+QString CheckFNIS::generateIdentifier() const
+{
+  QMap<QString, QString> fileList;
+
+  findRelevantFilesRecursive("meshes\\actors", fileList);
+
+  QStringList flattenedList;
+  for (auto iter = fileList.begin(); iter != fileList.end(); ++iter) {
+    flattenedList.append(iter.key() + "=" + iter.value());
+  }
+
+  return QCryptographicHash::hash(flattenedList.join(",").toUtf8(),
+                                  QCryptographicHash::Md5)
+      .toHex();
+}
+
+bool CheckFNIS::appIsFNIS(QString const& application, QString const& fnisApp)
+{
+  return QString::compare(QDir::fromNativeSeparators(application),
+                          QDir::fromNativeSeparators(fnisApp),
+                          Qt::CaseInsensitive) == 0;
+}
+
+QString CheckFNIS::getFnisPath() const
+{
+  if (!m_MOInfo->pluginSetting(name(), "enabled").toBool()) {
+    return "";
+  }
+
+  // Check if it's actually installed (...)
+  QStringList fnisBinaryList = m_MOInfo->findFiles(
+      "tools/GenerateFNIS_for_Users", [](const QString& fileName) -> bool {
+        return fileName.endsWith("GenerateFNISforUsers.exe", Qt::CaseInsensitive);
+      });
+
+  if (fnisBinaryList.count() == 0) {
+    // fnis seems not to be installed even though this is enabled
+    qDebug("fnis not installed");
+    return "";
+  }
+
+  // As this is looking in the vfs, there can be precisely 0 or 1 instances of FNIS
+  return fnisBinaryList.at(0);
+}
+
+bool CheckFNIS::fnisCheck(const QString& application)
+{
+
+  QString fnisApp(getFnisPath());
+  if (fnisApp.isEmpty() || appIsFNIS(application, fnisApp)) {
+    return true;
+  }
+
+  // prevent this check from being called recursively
+  if (m_Active) {
+    return true;
+  }
+
+  m_Active = true;
+  ON_BLOCK_EXIT([&] {
+    m_Active = false;
+  });
+
+  QString const newHash = generateIdentifier();
+
+  if (newHash == m_MOInfo->persistent(name(), m_MOInfo->profileName(), "").toString()) {
+    // Don't need to run fnis as nothing relevant has changed.
+    return true;
+  }
+
+  QDialogButtonBox::StandardButton res = QuestionBoxMemory::query(
+      nullptr, "fnisCheck", QFileInfo(application).fileName(),
+      tr("Run FNIS before %1?").arg(application),
+      tr("FNIS source data has been changed. You should run GenerateFNIS.exe now."),
+      QDialogButtonBox::Yes | QDialogButtonBox::No | QDialogButtonBox::Cancel,
+      QDialogButtonBox::Yes);
+
+  if (res == QDialogButtonBox::Yes) {
+    HANDLE process = m_MOInfo->startApplication(fnisApp);
+    bool cont      = true;
+    if (process == INVALID_HANDLE_VALUE) {
+      reportError(tr("Failed to start %1").arg(fnisApp));
+    } else {
+      DWORD exitCodeU;
+      if (m_MOInfo->waitForApplication(process, &exitCodeU)) {
+        int exitCode = static_cast<int>(exitCodeU);
+        if (exitCode != 0) {
+          cont = QMessageBox::question(
+                     nullptr, tr("Start %1?").arg(application),
+                     tr("FNIS reported a %1, do you want to run the application "
+                        "anyway?")
+                         .arg(exitCode < 0 ? tr("warning") : tr("critical error")),
+                     QMessageBox::Yes | QMessageBox::No,
+                     QMessageBox::No) == QMessageBox::Yes;
+        }
+      } else {
+        cont = QMessageBox::question(nullptr, tr("Start %1?").arg(application),
+                                     tr("Failed to determine FNIS exit code, do you "
+                                        "want to run the application "
+                                        "anyway?"),
+                                     QMessageBox::Yes | QMessageBox::No,
+                                     QMessageBox::No) == QMessageBox::Yes;
+      }
+      if (cont) {
+        m_MOInfo->setPersistent(name(), m_MOInfo->profileName(), newHash);
+      }
+    }
+    return cont;
+  } else if (res == QDialogButtonBox::No) {
+    return true;
+  } else {
+    // Don't run the app if they pressed cancel
+    return false;
+  }
+}
+
+void CheckFNIS::fnisEndCheck(const QString& application, unsigned int code)
+{
+  if (appIsFNIS(application, getFnisPath())) {
+    bool update  = true;
+    int exitCode = static_cast<int>(code);
+    if (exitCode != 0) {
+      update =
+          QMessageBox::question(
+              nullptr, tr("Start %1?").arg(application),
+              tr("FNIS reported a %1. Do you want to assume it worked?")
+                  .arg(exitCode < 0 ? tr("warning") : tr("critical error")),
+              QMessageBox::Yes | QMessageBox::No, QMessageBox::No) == QMessageBox::Yes;
+    }
+    if (update) {
+      m_MOInfo->setPersistent(name(), m_MOInfo->profileName(), generateIdentifier());
+    }
+  }
+}
+
+#if QT_VERSION < QT_VERSION_CHECK(5, 0, 0)
+Q_EXPORT_PLUGIN2(checkfnis, CheckFNIS)
+#endif
diff --git a/libs/check_fnis/src/checkfnis.h b/libs/check_fnis/src/checkfnis.h
new file mode 100644
index 0000000..8971ab2
--- /dev/null
+++ b/libs/check_fnis/src/checkfnis.h
@@ -0,0 +1,67 @@
+#ifndef CHECKFNIS_H
+#define CHECKFNIS_H
+
+#include <uibase/imoinfo.h>
+#include <uibase/iplugin.h>
+#include <uibase/versioninfo.h>
+
+#include <QList>
+#include <QMap>
+#include <QObject>
+#include <QString>
+
+#include <QtGlobal>  // for QT_VERSION, QT_VERSION_CHECK
+
+#include <vector>
+
+namespace MOBase
+{
+struct PluginSetting;
+}
+
+class CheckFNIS : public QObject, public MOBase::IPlugin
+{
+
+  Q_OBJECT
+  Q_INTERFACES(MOBase::IPlugin)
+#if QT_VERSION >= QT_VERSION_CHECK(5, 0, 0)
+  Q_PLUGIN_METADATA(IID "org.tannin.CheckFNIS")
+#endif
+
+public:
+  CheckFNIS();
+  ~CheckFNIS();
+
+public:  // IPlugin
+  virtual bool init(MOBase::IOrganizer* moInfo) override;
+  virtual QString name() const override;
+  virtual QString localizedName() const override;
+  virtual std::vector<std::shared_ptr<const MOBase::IPluginRequirement>>
+  requirements() const override;
+  virtual QString author() const override;
+  virtual QString description() const override;
+  virtual MOBase::VersionInfo version() const override;
+  virtual QList<MOBase::PluginSetting> settings() const override;
+
+private:
+  bool fnisCheck(const QString& application);
+  void fnisEndCheck(const QString& application, unsigned int code);
+
+  QString getFnisPath() const;
+  static bool appIsFNIS(QString const& application, const QString& fnisApp);
+
+  bool testFileRelevant(const MOBase::IOrganizer::FileInfo& fileName) const;
+  void findRelevantFilesRecursive(const QString& path,
+                                  QMap<QString, QString>& fileList) const;
+  // generates a map of file-names and hashes. Any change prompts a new fnis run
+  QString generateIdentifier() const;
+
+private:
+  MOBase::IOrganizer* m_MOInfo;
+  bool m_Active;
+
+  std::vector<QRegularExpression> const m_MatchExpressions;
+  std::vector<QRegularExpression> const m_SensitiveMatchExpressions;
+};
+
+#endif  // CHECKFNIS_H
diff --git a/libs/check_fnis/vcpkg.json b/libs/check_fnis/vcpkg.json
new file mode 100644
index 0000000..a639ce6
--- /dev/null
+++ b/libs/check_fnis/vcpkg.json
@@ -0,0 +1,15 @@
+{
+  "features": {
+    "standalone": {
+      "description": "Build Standalone.",
+      "dependencies": ["mo2-cmake"]
+    }
+  },
+  "vcpkg-configuration": {
+    "default-registry": {
+      "kind": "git",
+      "repository": "https://github.com/ModOrganizer2/vcpkg-registry",
+      "baseline": "8beb2e0efa9c17dd6d17bb05288dd1e40727f673"
+    }
+  }
+}