From 83e0cc45f4ccf1d170a6aa6054a99f61db8b1dbd Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 12:45:54 +0800
Subject: [PATCH 01/16] core/file_sys: Make RomFSReader an abstract interface

The original RomFSReader is renamed to DirectRomFSReader that directly reads the RomFS.
---
 src/core/file_sys/romfs_reader.cpp |  2 +-
 src/core/file_sys/romfs_reader.h   | 24 ++++++++++++++++++------
 2 files changed, 19 insertions(+), 7 deletions(-)

diff --git a/src/core/file_sys/romfs_reader.cpp b/src/core/file_sys/romfs_reader.cpp
index 8e624cbfc..64374684a 100644
--- a/src/core/file_sys/romfs_reader.cpp
+++ b/src/core/file_sys/romfs_reader.cpp
@@ -5,7 +5,7 @@
 
 namespace FileSys {
 
-std::size_t RomFSReader::ReadFile(std::size_t offset, std::size_t length, u8* buffer) {
+std::size_t DirectRomFSReader::ReadFile(std::size_t offset, std::size_t length, u8* buffer) {
     if (length == 0)
         return 0; // Crypto++ does not like zero size buffer
     file.Seek(file_offset + offset, SEEK_SET);
diff --git a/src/core/file_sys/romfs_reader.h b/src/core/file_sys/romfs_reader.h
index 72a02cde3..5ee39015b 100644
--- a/src/core/file_sys/romfs_reader.h
+++ b/src/core/file_sys/romfs_reader.h
@@ -6,23 +6,35 @@
 
 namespace FileSys {
 
+/**
+ * Interface for reading RomFS data.
+ */
 class RomFSReader {
 public:
-    RomFSReader(FileUtil::IOFile&& file, std::size_t file_offset, std::size_t data_size)
+    virtual std::size_t GetSize() const = 0;
+    virtual std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) = 0;
+};
+
+/**
+ * A RomFS reader that directly reads the RomFS file.
+ */
+class DirectRomFSReader : public RomFSReader {
+public:
+    DirectRomFSReader(FileUtil::IOFile&& file, std::size_t file_offset, std::size_t data_size)
         : is_encrypted(false), file(std::move(file)), file_offset(file_offset),
           data_size(data_size) {}
 
-    RomFSReader(FileUtil::IOFile&& file, std::size_t file_offset, std::size_t data_size,
-                const std::array<u8, 16>& key, const std::array<u8, 16>& ctr,
-                std::size_t crypto_offset)
+    DirectRomFSReader(FileUtil::IOFile&& file, std::size_t file_offset, std::size_t data_size,
+                      const std::array<u8, 16>& key, const std::array<u8, 16>& ctr,
+                      std::size_t crypto_offset)
         : is_encrypted(true), file(std::move(file)), key(key), ctr(ctr), file_offset(file_offset),
           crypto_offset(crypto_offset), data_size(data_size) {}
 
-    std::size_t GetSize() const {
+    std::size_t GetSize() const override {
         return data_size;
     }
 
-    std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer);
+    std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) override;
 
 private:
     bool is_encrypted;

From 890405bb7cdb404a0f84189d09d04ee7930559c6 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 12:54:07 +0800
Subject: [PATCH 02/16] core/file_sys: LayeredFS implementation

This implementation is different from Luma3DS's which directly hooks the SDK functions. Instead, we read the RomFS's metadata and figure out the directory and file structure. Then, relocations (i.e. replacements/deletions/patches) are applied. Afterwards, we rebuild the metadata, and assign 'fake' data offsets to the files. When we want to read file data from this rebuilt RomFS, we use binary search to find the last data offset smaller or equal to the given offset and read from that file  (either from the original RomFS, or from replacement files, or from buffered data with patches applied) and any later files when length is not enough.

The code that rebuilds the metadata is pretty complex and uses quite a few variables to keep track of necessary information like metadata offsets. According to my tests, it is able to build RomFS-es identical to the original (but without trailing garbage data) when no relocations are applied.
---
 src/core/CMakeLists.txt          |   2 +
 src/core/file_sys/layered_fs.cpp | 551 +++++++++++++++++++++++++++++++
 src/core/file_sys/layered_fs.h   | 117 +++++++
 3 files changed, 670 insertions(+)
 create mode 100644 src/core/file_sys/layered_fs.cpp
 create mode 100644 src/core/file_sys/layered_fs.h

diff --git a/src/core/CMakeLists.txt b/src/core/CMakeLists.txt
index 064e44f94..d5b2d2f47 100644
--- a/src/core/CMakeLists.txt
+++ b/src/core/CMakeLists.txt
@@ -72,6 +72,8 @@ add_library(core STATIC
     file_sys/delay_generator.h
     file_sys/ivfc_archive.cpp
     file_sys/ivfc_archive.h
+    file_sys/layered_fs.cpp
+    file_sys/layered_fs.h
     file_sys/ncch_container.cpp
     file_sys/ncch_container.h
     file_sys/patch.cpp
diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
new file mode 100644
index 000000000..9a194569a
--- /dev/null
+++ b/src/core/file_sys/layered_fs.cpp
@@ -0,0 +1,551 @@
+// Copyright 2020 Citra Emulator Project
+// Licensed under GPLv2 or any later version
+// Refer to the license.txt file included.
+
+#include <algorithm>
+#include <cstring>
+#include "common/alignment.h"
+#include "common/assert.h"
+#include "common/common_paths.h"
+#include "common/file_util.h"
+#include "common/string_util.h"
+#include "common/swap.h"
+#include "core/file_sys/layered_fs.h"
+#include "core/file_sys/patch.h"
+
+namespace FileSys {
+
+struct FileRelocationInfo {
+    int type;                      // 0 - none, 1 - replaced / created, 2 - patched, 3 - removed
+    u64 original_offset;           // Type 0. Offset is absolute
+    FileUtil::IOFile replace_file; // Type 1
+    std::vector<u8> patched_file;  // Type 2
+    u64 size;                      // Relocated file size
+};
+struct LayeredFS::File {
+    std::string name;
+    std::string path;
+    FileRelocationInfo relocation{};
+    Directory* parent;
+};
+
+struct DirectoryMetadata {
+    u32_le parent_directory_offset;
+    u32_le next_sibling_offset;
+    u32_le first_child_directory_offset;
+    u32_le first_file_offset;
+    u32_le hash_bucket_next;
+    u32_le name_length;
+    // Followed by a name of name length (aligned up to 4)
+};
+static_assert(sizeof(DirectoryMetadata) == 0x18, "Size of DirectoryMetadata is not correct");
+
+struct FileMetadata {
+    u32_le parent_directory_offset;
+    u32_le next_sibling_offset;
+    u64_le file_data_offset;
+    u64_le file_data_length;
+    u32_le hash_bucket_next;
+    u32_le name_length;
+    // Followed by a name of name length (aligned up to 4)
+};
+static_assert(sizeof(FileMetadata) == 0x20, "Size of FileMetadata is not correct");
+
+LayeredFS::LayeredFS(std::shared_ptr<RomFSReader> romfs_, std::string patch_path_,
+                     std::string patch_ext_path_)
+    : romfs(std::move(romfs_)), patch_path(std::move(patch_path_)),
+      patch_ext_path(std::move(patch_ext_path_)) {
+
+    romfs->ReadFile(0, sizeof(header), reinterpret_cast<u8*>(&header));
+
+    ASSERT_MSG(header.header_length == sizeof(header), "Header size is incorrect");
+
+    // TODO: is root always the first directory in table?
+    root.parent = &root;
+    LoadDirectory(root, 0);
+
+    LoadRelocations();
+    LoadExtRelocations();
+
+    RebuildMetadata();
+}
+
+LayeredFS::~LayeredFS() = default;
+
+void LayeredFS::LoadDirectory(Directory& current, u32 offset) {
+    DirectoryMetadata metadata;
+    romfs->ReadFile(header.directory_metadata_table.offset + offset, sizeof(metadata),
+                    reinterpret_cast<u8*>(&metadata));
+
+    current.name = ReadName(header.directory_metadata_table.offset + offset + sizeof(metadata),
+                            metadata.name_length);
+    current.path = current.parent->path + current.name + DIR_SEP;
+    directory_path_map.emplace(current.path, &current);
+
+    if (metadata.first_file_offset != 0xFFFFFFFF) {
+        LoadFile(current, metadata.first_file_offset);
+    }
+
+    if (metadata.first_child_directory_offset != 0xFFFFFFFF) {
+        auto child = std::make_unique<Directory>();
+        auto& directory = *child;
+        directory.parent = &current;
+        current.directories.emplace_back(std::move(child));
+        LoadDirectory(directory, metadata.first_child_directory_offset);
+    }
+
+    if (metadata.next_sibling_offset != 0xFFFFFFFF) {
+        auto sibling = std::make_unique<Directory>();
+        auto& directory = *sibling;
+        directory.parent = current.parent;
+        current.parent->directories.emplace_back(std::move(sibling));
+        LoadDirectory(directory, metadata.next_sibling_offset);
+    }
+}
+
+void LayeredFS::LoadFile(Directory& parent, u32 offset) {
+    FileMetadata metadata;
+    romfs->ReadFile(header.file_metadata_table.offset + offset, sizeof(metadata),
+                    reinterpret_cast<u8*>(&metadata));
+
+    auto file = std::make_unique<File>();
+    file->name = ReadName(header.file_metadata_table.offset + offset + sizeof(metadata),
+                          metadata.name_length);
+    file->path = parent.path + file->name;
+    file->relocation.original_offset = header.file_data_offset + metadata.file_data_offset;
+    file->relocation.size = metadata.file_data_length;
+    file->parent = &parent;
+
+    file_path_map.emplace(file->path, file.get());
+    parent.files.emplace_back(std::move(file));
+
+    if (metadata.next_sibling_offset != 0xFFFFFFFF) {
+        LoadFile(parent, metadata.next_sibling_offset);
+    }
+}
+
+std::string LayeredFS::ReadName(u32 offset, u32 name_length) {
+    std::vector<u16_le> buffer(name_length / sizeof(u16_le));
+    romfs->ReadFile(offset, name_length, reinterpret_cast<u8*>(buffer.data()));
+
+    std::u16string name(buffer.size(), 0);
+    std::transform(buffer.begin(), buffer.end(), name.begin(), [](u16_le character) {
+        return static_cast<char16_t>(static_cast<u16>(character));
+    });
+    return Common::UTF16ToUTF8(name);
+}
+
+void LayeredFS::LoadRelocations() {
+    if (!FileUtil::Exists(patch_path)) {
+        return;
+    }
+
+    const FileUtil::DirectoryEntryCallable callback = [this,
+                                                       &callback](u64* /*num_entries_out*/,
+                                                                  const std::string& directory,
+                                                                  const std::string& virtual_name) {
+        auto* parent = directory_path_map.at(directory.substr(patch_path.size() - 1));
+
+        if (FileUtil::IsDirectory(directory + virtual_name + DIR_SEP)) {
+            const auto path = (directory + virtual_name + DIR_SEP).substr(patch_path.size() - 1);
+            if (!directory_path_map.count(path)) { // Add this directory
+                auto directory = std::make_unique<Directory>();
+                directory->name = virtual_name;
+                directory->path = path;
+                directory->parent = parent;
+                directory_path_map.emplace(path, directory.get());
+                parent->directories.emplace_back(std::move(directory));
+                LOG_INFO(Service_FS, "LayeredFS created directory {}", path);
+            }
+            return FileUtil::ForeachDirectoryEntry(nullptr, directory + virtual_name + DIR_SEP,
+                                                   callback);
+        }
+
+        const auto path = (directory + virtual_name).substr(patch_path.size() - 1);
+        if (!file_path_map.count(path)) { // Newly created file
+            auto file = std::make_unique<File>();
+            file->name = virtual_name;
+            file->path = path;
+            file->parent = parent;
+            file_path_map.emplace(path, file.get());
+            parent->files.emplace_back(std::move(file));
+            LOG_INFO(Service_FS, "LayeredFS created file {}", path);
+        }
+
+        auto* file = file_path_map.at(path);
+        file->relocation.replace_file = FileUtil::IOFile(directory + virtual_name, "rb");
+        if (file->relocation.replace_file) {
+            file->relocation.type = 1;
+            file->relocation.size = file->relocation.replace_file.GetSize();
+            LOG_INFO(Service_FS, "LayeredFS replacement file in use for {}", path);
+        } else {
+            LOG_ERROR(Service_FS, "Could not open replacement file for {}", path);
+        }
+        return true;
+    };
+
+    FileUtil::ForeachDirectoryEntry(nullptr, patch_path, callback);
+}
+
+void LayeredFS::LoadExtRelocations() {
+    if (!FileUtil::Exists(patch_ext_path)) {
+        return;
+    }
+
+    if (patch_ext_path.back() == '/' || patch_ext_path.back() == '\\') {
+        // ScanDirectoryTree expects a path without trailing '/'
+        patch_ext_path.erase(patch_ext_path.size() - 1, 1);
+    }
+
+    FileUtil::FSTEntry result;
+    FileUtil::ScanDirectoryTree(patch_ext_path, result, 256);
+
+    for (const auto& entry : result.children) {
+        if (FileUtil::IsDirectory(entry.physicalName)) {
+            continue;
+        }
+
+        const auto path = entry.physicalName.substr(patch_ext_path.size());
+        if (path.size() >= 5 && path.substr(path.size() - 5) == ".stub") {
+            // Remove the corresponding file if exists
+            const auto file_path = path.substr(0, path.size() - 5);
+            if (file_path_map.count(file_path)) {
+                auto& file = *file_path_map[file_path];
+                file.relocation.type = 3;
+                file.relocation.size = 0;
+                file_path_map.erase(file_path);
+                LOG_INFO(Service_FS, "LayeredFS removed file {}", file_path);
+            } else {
+                LOG_WARNING(Service_FS, "LayeredFS file for stub {} not found", path);
+            }
+        } else if (path.size() >= 4) {
+            const auto extension = path.substr(path.size() - 4);
+            if (extension != ".ips" && extension != ".bps") {
+                LOG_WARNING(Service_FS, "LayeredFS unknown ext file {}", path);
+            }
+
+            const auto file_path = path.substr(0, path.size() - 4);
+            if (!file_path_map.count(file_path)) {
+                LOG_WARNING(Service_FS, "LayeredFS original file for patch {} not found", path);
+                continue;
+            }
+
+            FileUtil::IOFile patch_file(entry.physicalName, "rb");
+            if (!patch_file) {
+                LOG_ERROR(Service_FS, "LayeredFS Could not open file {}", entry.physicalName);
+                continue;
+            }
+
+            const auto size = patch_file.GetSize();
+            std::vector<u8> patch(size);
+            if (patch_file.ReadBytes(patch.data(), size) != size) {
+                LOG_ERROR(Service_FS, "LayeredFS Could not read file {}", entry.physicalName);
+                continue;
+            }
+
+            auto& file = *file_path_map[file_path];
+            std::vector<u8> buffer(file.relocation.size); // Original size
+            romfs->ReadFile(file.relocation.original_offset, buffer.size(), buffer.data());
+
+            bool ret = false;
+            if (extension == ".ips") {
+                ret = Patch::ApplyIpsPatch(patch, buffer);
+            } else {
+                ret = Patch::ApplyBpsPatch(patch, buffer);
+            }
+
+            if (ret) {
+                LOG_INFO(Service_FS, "LayeredFS patched file {}", file_path);
+
+                file.relocation.type = 2;
+                file.relocation.size = buffer.size();
+                file.relocation.patched_file = std::move(buffer);
+            } else {
+                LOG_ERROR(Service_FS, "LayeredFS failed to patch file {}", file_path);
+            }
+        } else {
+            LOG_WARNING(Service_FS, "LayeredFS unknown ext file {}", path);
+        }
+    }
+}
+
+std::size_t GetNameSize(const std::string& name) {
+    std::u16string u16name = Common::UTF8ToUTF16(name);
+    return Common::AlignUp(u16name.size() * 2, 4);
+}
+
+void LayeredFS::PrepareBuildDirectory(Directory& current) {
+    directory_metadata_offset_map.emplace(&current, current_directory_offset);
+    directory_list.emplace_back(&current);
+    current_directory_offset += sizeof(DirectoryMetadata) + GetNameSize(current.name);
+}
+
+void LayeredFS::PrepareBuildFile(File& current) {
+    if (current.relocation.type == 3) { // Deleted files are not counted
+        return;
+    }
+    file_metadata_offset_map.emplace(&current, current_file_offset);
+    file_list.emplace_back(&current);
+    current_file_offset += sizeof(FileMetadata) + GetNameSize(current.name);
+}
+
+void LayeredFS::PrepareBuild(Directory& current) {
+    for (const auto& child : current.files) {
+        PrepareBuildFile(*child);
+    }
+
+    for (const auto& child : current.directories) {
+        PrepareBuildDirectory(*child);
+    }
+
+    for (const auto& child : current.directories) {
+        PrepareBuild(*child);
+    }
+}
+
+// Implementation from 3dbrew
+u32 CalcHash(const std::string& name, u32 parent_offset) {
+    u32 hash = parent_offset ^ 123456789;
+
+    std::u16string u16name = Common::UTF8ToUTF16(name);
+    std::vector<u16_le> tmp_buffer(u16name.size());
+    std::transform(u16name.begin(), u16name.end(), tmp_buffer.begin(), [](char16_t character) {
+        return static_cast<u16_le>(static_cast<u16>(character));
+    });
+
+    std::vector<u8> buffer(tmp_buffer.size() * 2);
+    std::memcpy(buffer.data(), tmp_buffer.data(), buffer.size());
+    for (std::size_t i = 0; i < buffer.size(); i += 2) {
+        hash = (hash >> 5) | (hash << 27);
+        hash ^= static_cast<u16>((buffer[i]) | (buffer[i + 1] << 8));
+    }
+    return hash;
+}
+
+std::size_t WriteName(u8* dest, std::u16string name) {
+    const auto buffer_size = Common::AlignUp(name.size() * 2, 4);
+    std::vector<u16_le> buffer(buffer_size / 2);
+    std::transform(name.begin(), name.end(), buffer.begin(), [](char16_t character) {
+        return static_cast<u16_le>(static_cast<u16>(character));
+    });
+    std::memcpy(dest, buffer.data(), buffer_size);
+
+    return buffer_size;
+}
+
+void LayeredFS::BuildDirectories() {
+    directory_metadata_table.resize(current_directory_offset, 0xFF);
+
+    std::size_t written = 0;
+    for (const auto& directory : directory_list) {
+        DirectoryMetadata metadata;
+        std::memset(&metadata, 0xFF, sizeof(metadata));
+        metadata.parent_directory_offset = directory_metadata_offset_map.at(directory->parent);
+
+        if (directory->parent != directory) {
+            bool flag = false;
+            for (const auto& sibling : directory->parent->directories) {
+                if (flag) {
+                    metadata.next_sibling_offset = directory_metadata_offset_map.at(sibling.get());
+                    break;
+                } else if (sibling.get() == directory) {
+                    flag = true;
+                }
+            }
+        }
+
+        if (!directory->directories.empty()) {
+            metadata.first_child_directory_offset =
+                directory_metadata_offset_map.at(directory->directories.front().get());
+        }
+
+        if (!directory->files.empty()) {
+            metadata.first_file_offset =
+                file_metadata_offset_map.at(directory->files.front().get());
+        }
+
+        const auto bucket = CalcHash(directory->name, metadata.parent_directory_offset) %
+                            directory_hash_table.size();
+        metadata.hash_bucket_next = directory_hash_table[bucket];
+        directory_hash_table[bucket] = directory_metadata_offset_map.at(directory);
+
+        // Write metadata and name
+        std::u16string u16name = Common::UTF8ToUTF16(directory->name);
+        metadata.name_length = u16name.size() * 2;
+
+        std::memcpy(directory_metadata_table.data() + written, &metadata, sizeof(metadata));
+        written += sizeof(metadata);
+
+        written += WriteName(directory_metadata_table.data() + written, u16name);
+    }
+
+    ASSERT_MSG(written == directory_metadata_table.size(),
+               "Calculated size for directory metadata table is wrong");
+}
+
+void LayeredFS::BuildFiles() {
+    file_metadata_table.resize(current_file_offset, 0xFF);
+
+    std::size_t written = 0;
+    for (const auto& file : file_list) {
+        FileMetadata metadata;
+        std::memset(&metadata, 0xFF, sizeof(metadata));
+
+        metadata.parent_directory_offset = directory_metadata_offset_map.at(file->parent);
+
+        bool flag = false;
+        for (const auto& sibling : file->parent->files) {
+            if (sibling->relocation.type == 3) { // removed file
+                continue;
+            }
+            if (flag) {
+                metadata.next_sibling_offset = file_metadata_offset_map.at(sibling.get());
+                break;
+            } else if (sibling.get() == file) {
+                flag = true;
+            }
+        }
+
+        metadata.file_data_offset = current_data_offset;
+        metadata.file_data_length = file->relocation.size;
+        current_data_offset += Common::AlignUp(metadata.file_data_length, 16);
+        if (metadata.file_data_length != 0) {
+            data_offset_map.emplace(metadata.file_data_offset, file);
+        }
+
+        const auto bucket =
+            CalcHash(file->name, metadata.parent_directory_offset) % file_hash_table.size();
+        metadata.hash_bucket_next = file_hash_table[bucket];
+        file_hash_table[bucket] = file_metadata_offset_map.at(file);
+
+        // Write metadata and name
+        std::u16string u16name = Common::UTF8ToUTF16(file->name);
+        metadata.name_length = u16name.size() * 2;
+
+        std::memcpy(file_metadata_table.data() + written, &metadata, sizeof(metadata));
+        written += sizeof(metadata);
+
+        written += WriteName(file_metadata_table.data() + written, u16name);
+    }
+
+    ASSERT_MSG(written == file_metadata_table.size(),
+               "Calculated size for file metadata table is wrong");
+}
+
+// Implementation from 3dbrew
+std::size_t GetHashTableSize(std::size_t entry_count) {
+    if (entry_count < 3) {
+        return 3;
+    } else if (entry_count < 19) {
+        return entry_count | 1;
+    } else {
+        std::size_t count = entry_count;
+        while (count % 2 == 0 || count % 3 == 0 || count % 5 == 0 || count % 7 == 0 ||
+               count % 11 == 0 || count % 13 == 0 || count % 17 == 0) {
+            count++;
+        }
+        return count;
+    }
+}
+
+void LayeredFS::RebuildMetadata() {
+    PrepareBuildDirectory(root);
+    PrepareBuild(root);
+
+    directory_hash_table.resize(GetHashTableSize(directory_list.size()), 0xFFFFFFFF);
+    file_hash_table.resize(GetHashTableSize(file_list.size()), 0xFFFFFFFF);
+
+    BuildDirectories();
+    BuildFiles();
+
+    // Create header
+    RomFSHeader header;
+    header.header_length = sizeof(header);
+    header.directory_hash_table = {
+        /*offset*/ sizeof(header),
+        /*length*/ static_cast<u32_le>(directory_hash_table.size() * sizeof(u32_le))};
+    header.directory_metadata_table = {
+        /*offset*/
+        header.directory_hash_table.offset + header.directory_hash_table.length,
+        /*length*/ static_cast<u32_le>(directory_metadata_table.size())};
+    header.file_hash_table = {
+        /*offset*/
+        header.directory_metadata_table.offset + header.directory_metadata_table.length,
+        /*length*/ static_cast<u32_le>(file_hash_table.size() * sizeof(u32_le))};
+    header.file_metadata_table = {/*offset*/ header.file_hash_table.offset +
+                                      header.file_hash_table.length,
+                                  /*length*/ static_cast<u32_le>(file_metadata_table.size())};
+    header.file_data_offset =
+        Common::AlignUp(header.file_metadata_table.offset + header.file_metadata_table.length, 16);
+
+    // Write hash table and metadata table
+    metadata.resize(header.file_data_offset);
+    std::memcpy(metadata.data(), &header, header.header_length);
+    std::memcpy(metadata.data() + header.directory_hash_table.offset, directory_hash_table.data(),
+                header.directory_hash_table.length);
+    std::memcpy(metadata.data() + header.directory_metadata_table.offset,
+                directory_metadata_table.data(), header.directory_metadata_table.length);
+    std::memcpy(metadata.data() + header.file_hash_table.offset, file_hash_table.data(),
+                header.file_hash_table.length);
+    std::memcpy(metadata.data() + header.file_metadata_table.offset, file_metadata_table.data(),
+                header.file_metadata_table.length);
+}
+
+std::size_t LayeredFS::GetSize() const {
+    return metadata.size() + current_data_offset;
+}
+
+std::size_t LayeredFS::ReadFile(std::size_t offset, std::size_t length, u8* buffer) {
+    ASSERT_MSG(offset + length <= GetSize(), "Out of bound");
+
+    std::size_t read_size = 0;
+    if (offset < metadata.size()) {
+        // First read the metadata
+        const auto to_read = std::min(metadata.size() - offset, length);
+        std::memcpy(buffer, metadata.data() + offset, to_read);
+        read_size += to_read;
+        offset = 0;
+    } else {
+        offset -= metadata.size();
+    }
+
+    // Read files
+    auto current = (--data_offset_map.upper_bound(offset));
+    while (read_size < length) {
+        const auto relative_offset = offset - current->first;
+        std::size_t to_read{};
+        if (current->second->relocation.size > relative_offset) {
+            to_read =
+                std::min(current->second->relocation.size - relative_offset, length - read_size);
+        }
+        const auto alignment =
+            std::min(Common::AlignUp(current->second->relocation.size, 16) - relative_offset,
+                     length - read_size) -
+            to_read;
+
+        // Read the file in different ways depending on relocation type
+        auto& relocation = current->second->relocation;
+        if (relocation.type == 0) { // none
+            romfs->ReadFile(relocation.original_offset + relative_offset, to_read,
+                            buffer + read_size);
+        } else if (relocation.type == 1) { // replace
+            relocation.replace_file.Seek(relative_offset, SEEK_SET);
+            relocation.replace_file.ReadBytes(buffer + read_size, to_read);
+        } else if (relocation.type == 2) { // patch
+            std::memcpy(buffer + read_size, relocation.patched_file.data() + relative_offset,
+                        to_read);
+        } else {
+            UNREACHABLE();
+        }
+
+        std::memset(buffer + read_size + to_read, 0, alignment);
+
+        read_size += to_read + alignment;
+        offset += to_read + alignment;
+        current++;
+    }
+
+    return read_size;
+}
+
+} // namespace FileSys
diff --git a/src/core/file_sys/layered_fs.h b/src/core/file_sys/layered_fs.h
new file mode 100644
index 000000000..b9dcb831f
--- /dev/null
+++ b/src/core/file_sys/layered_fs.h
@@ -0,0 +1,117 @@
+// Copyright 2020 Citra Emulator Project
+// Licensed under GPLv2 or any later version
+// Refer to the license.txt file included.
+
+#pragma once
+
+#include <map>
+#include <memory>
+#include <string>
+#include <unordered_map>
+#include <vector>
+#include "common/common_types.h"
+#include "common/swap.h"
+#include "core/file_sys/romfs_reader.h"
+
+namespace FileSys {
+
+struct RomFSHeader {
+    struct Descriptor {
+        u32_le offset;
+        u32_le length;
+    };
+    u32_le header_length;
+    Descriptor directory_hash_table;
+    Descriptor directory_metadata_table;
+    Descriptor file_hash_table;
+    Descriptor file_metadata_table;
+    u32_le file_data_offset;
+};
+static_assert(sizeof(RomFSHeader) == 0x28, "Size of RomFSHeader is not correct");
+
+/**
+ * LayeredFS implementation. This basically adds a layer to another RomFSReader.
+ *
+ * patch_path: Path for RomFS replacements. Files present in this path replace or create
+ * corresponding files in RomFS.
+ * patch_ext_path: Path for RomFS extensions. Files present in this path:
+ *  - When with an extension of ".stub", remove the corresponding file in the RomFS.
+ *  - When with an extension of ".ips" or ".bps", patch the file in the RomFS.
+ */
+class LayeredFS : public RomFSReader {
+public:
+    explicit LayeredFS(std::shared_ptr<RomFSReader> romfs, std::string patch_path,
+                       std::string patch_ext_path);
+    ~LayeredFS();
+
+    std::size_t GetSize() const override;
+    std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) override;
+
+private:
+    struct File;
+    struct Directory {
+        std::string name;
+        std::string path; // with trailing '/'
+        std::vector<std::unique_ptr<File>> files;
+        std::vector<std::unique_ptr<Directory>> directories;
+        Directory* parent;
+    };
+
+    std::string ReadName(u32 offset, u32 name_length);
+
+    // Loads the current directory, then its siblings, and then its children.
+    void LoadDirectory(Directory& current, u32 offset);
+
+    // Load the file at offset, and then its siblings.
+    void LoadFile(Directory& parent, u32 offset);
+
+    // Load replace/create relocations
+    void LoadRelocations();
+
+    // Load patch/remove relocations
+    void LoadExtRelocations();
+
+    // Calculate the offset of a single directory add it to the map and list of directories
+    void PrepareBuildDirectory(Directory& current);
+
+    // Calculate the offset of a single file add it to the map and list of files
+    void PrepareBuildFile(File& current);
+
+    // Recursively generate a sequence of files and directories and their offsets for all
+    // children of current. (The current directory itself is not handled.)
+    void PrepareBuild(Directory& current);
+
+    void BuildDirectories();
+    void BuildFiles();
+
+    void RebuildMetadata();
+
+    std::shared_ptr<RomFSReader> romfs;
+    std::string patch_path;
+    std::string patch_ext_path;
+
+    RomFSHeader header;
+    Directory root;
+    std::unordered_map<std::string, File*> file_path_map;
+    std::unordered_map<std::string, Directory*> directory_path_map;
+    std::map<u64, File*> data_offset_map; // assigned data offset -> file
+    std::vector<u8> metadata;             // Includes header, hash table and metadata
+
+    // Used for rebuilding header
+    std::vector<u32_le> directory_hash_table;
+    std::vector<u32_le> file_hash_table;
+
+    std::unordered_map<Directory*, u32>
+        directory_metadata_offset_map;        // directory -> metadata offset
+    std::vector<Directory*> directory_list;   // sequence of directories to be written to metadata
+    u64 current_directory_offset{};           // current directory metadata offset
+    std::vector<u8> directory_metadata_table; // rebuilt directory metadata table
+
+    std::unordered_map<File*, u32> file_metadata_offset_map; // file -> metadata offset
+    std::vector<File*> file_list;        // sequence of files to be written to metadata
+    u64 current_file_offset{};           // current file metadata offset
+    std::vector<u8> file_metadata_table; // rebuilt file metadata table
+    u64 current_data_offset{};           // current assigned data offset
+};
+
+} // namespace FileSys

From 8a570bf00c7b0e709a73f64b78ad4daeb9765d17 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 13:45:10 +0800
Subject: [PATCH 03/16] core: Use LayeredFS while reading RomFS

Only enabled for NCCHs that do not have an override romfs.

LayeredFS files should be put in the `load` directory in User Directory. The directory structure is similar to yuzu's but currently does not allow named mods yet. Replacement files should be put in `load/mods/<Title ID>/romfs` while patches/stubs should be put in `load/mods/<Title ID>/romfs_ext`.
---
 src/core/file_sys/ncch_container.cpp | 28 +++++++++++++++++++++-------
 src/core/loader/3dsx.cpp             |  4 ++--
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index f0687fa9e..53432f945 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -11,6 +11,7 @@
 #include "common/common_types.h"
 #include "common/logging/log.h"
 #include "core/core.h"
+#include "core/file_sys/layered_fs.h"
 #include "core/file_sys/ncch_container.h"
 #include "core/file_sys/patch.h"
 #include "core/file_sys/seed_db.h"
@@ -597,12 +598,24 @@ Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romf
     if (!romfs_file_inner.IsOpen())
         return Loader::ResultStatus::Error;
 
+    std::shared_ptr<RomFSReader> direct_romfs;
     if (is_encrypted) {
-        romfs_file = std::make_shared<RomFSReader>(std::move(romfs_file_inner), romfs_offset,
-                                                   romfs_size, secondary_key, romfs_ctr, 0x1000);
+        direct_romfs =
+            std::make_shared<DirectRomFSReader>(std::move(romfs_file_inner), romfs_offset,
+                                                romfs_size, secondary_key, romfs_ctr, 0x1000);
     } else {
-        romfs_file =
-            std::make_shared<RomFSReader>(std::move(romfs_file_inner), romfs_offset, romfs_size);
+        direct_romfs = std::make_shared<DirectRomFSReader>(std::move(romfs_file_inner),
+                                                           romfs_offset, romfs_size);
+    }
+
+    const auto path =
+        fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                    ncch_header.program_id);
+    if (FileUtil::Exists(path + "romfs/") || FileUtil::Exists(path + "romfs_ext/")) {
+        romfs_file = std::make_shared<LayeredFS>(std::move(direct_romfs), path + "romfs/",
+                                                 path + "romfs_ext/");
+    } else {
+        romfs_file = std::move(direct_romfs);
     }
 
     return Loader::ResultStatus::Success;
@@ -614,9 +627,10 @@ Loader::ResultStatus NCCHContainer::ReadOverrideRomFS(std::shared_ptr<RomFSReade
     if (FileUtil::Exists(split_filepath)) {
         FileUtil::IOFile romfs_file_inner(split_filepath, "rb");
         if (romfs_file_inner.IsOpen()) {
-            LOG_WARNING(Service_FS, "File {} overriding built-in RomFS", split_filepath);
-            romfs_file = std::make_shared<RomFSReader>(std::move(romfs_file_inner), 0,
-                                                       romfs_file_inner.GetSize());
+            LOG_WARNING(Service_FS, "File {} overriding built-in RomFS; LayeredFS not enabled",
+                        split_filepath);
+            romfs_file = std::make_shared<DirectRomFSReader>(std::move(romfs_file_inner), 0,
+                                                             romfs_file_inner.GetSize());
             return Loader::ResultStatus::Success;
         }
     }
diff --git a/src/core/loader/3dsx.cpp b/src/core/loader/3dsx.cpp
index 7629ad376..84321011b 100644
--- a/src/core/loader/3dsx.cpp
+++ b/src/core/loader/3dsx.cpp
@@ -309,8 +309,8 @@ ResultStatus AppLoader_THREEDSX::ReadRomFS(std::shared_ptr<FileSys::RomFSReader>
         if (!romfs_file_inner.IsOpen())
             return ResultStatus::Error;
 
-        romfs_file = std::make_shared<FileSys::RomFSReader>(std::move(romfs_file_inner),
-                                                            romfs_offset, romfs_size);
+        romfs_file = std::make_shared<FileSys::DirectRomFSReader>(std::move(romfs_file_inner),
+                                                                  romfs_offset, romfs_size);
 
         return ResultStatus::Success;
     }

From 91e5a39a08adbb7d149fae29046a48a5c7329ff3 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 13:50:29 +0800
Subject: [PATCH 04/16] core/file_sys: Allow exefs mods to be read from mods
 path

The original path (file_name.exefsdir) is still supported, but alternatively users can choose to put exefs patches in the same place as LayeredFS files (`load/mods/<Title ID>/exefs`).
---
 src/core/file_sys/ncch_container.cpp | 35 ++++++++++++++++++++--------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index 53432f945..dcc8dd57b 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -513,7 +513,13 @@ Loader::ResultStatus NCCHContainer::ApplyCodePatch(std::vector<u8>& code) const
         std::string path;
         bool (*patch_fn)(const std::vector<u8>& patch, std::vector<u8>& code);
     };
-    const std::array<PatchLocation, 2> patch_paths{{
+
+    const auto mods_path =
+        fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                    ncch_header.program_id);
+    const std::array<PatchLocation, 4> patch_paths{{
+        {mods_path + "exefs/code.ips", Patch::ApplyIpsPatch},
+        {mods_path + "exefs/code.bps", Patch::ApplyBpsPatch},
         {filepath + ".exefsdir/code.ips", Patch::ApplyIpsPatch},
         {filepath + ".exefsdir/code.bps", Patch::ApplyBpsPatch},
     }};
@@ -552,17 +558,26 @@ Loader::ResultStatus NCCHContainer::LoadOverrideExeFSSection(const char* name,
     else
         return Loader::ResultStatus::Error;
 
-    std::string section_override = filepath + ".exefsdir/" + override_name;
-    FileUtil::IOFile section_file(section_override, "rb");
+    const auto mods_path =
+        fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                    ncch_header.program_id);
+    std::array<std::string, 2> override_paths{{
+        mods_path + "exefs/" + override_name,
+        filepath + ".exefsdir/" + override_name,
+    }};
 
-    if (section_file.IsOpen()) {
-        auto section_size = section_file.GetSize();
-        buffer.resize(section_size);
+    for (const auto& path : override_paths) {
+        FileUtil::IOFile section_file(path, "rb");
 
-        section_file.Seek(0, SEEK_SET);
-        if (section_file.ReadBytes(&buffer[0], section_size) == section_size) {
-            LOG_WARNING(Service_FS, "File {} overriding built-in ExeFS file", section_override);
-            return Loader::ResultStatus::Success;
+        if (section_file.IsOpen()) {
+            auto section_size = section_file.GetSize();
+            buffer.resize(section_size);
+
+            section_file.Seek(0, SEEK_SET);
+            if (section_file.ReadBytes(&buffer[0], section_size) == section_size) {
+                LOG_WARNING(Service_FS, "File {} overriding built-in ExeFS file", path);
+                return Loader::ResultStatus::Success;
+            }
         }
     }
     return Loader::ResultStatus::ErrorNotUsed;

From 7c652a0479406eac115b503b5edc67658a825448 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 14:44:34 +0800
Subject: [PATCH 05/16] citra_qt: Add 'Open Mods Location'

---
 src/citra_qt/game_list.cpp | 9 +++++++++
 src/citra_qt/game_list.h   | 3 ++-
 src/citra_qt/main.cpp      | 5 +++++
 3 files changed, 16 insertions(+), 1 deletion(-)

diff --git a/src/citra_qt/game_list.cpp b/src/citra_qt/game_list.cpp
index 2d5af1b0c..4ba7e99d6 100644
--- a/src/citra_qt/game_list.cpp
+++ b/src/citra_qt/game_list.cpp
@@ -468,6 +468,7 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
     QAction* open_texture_dump_location = context_menu.addAction(tr("Open Texture Dump Location"));
     QAction* open_texture_load_location =
         context_menu.addAction(tr("Open Custom Texture Location"));
+    QAction* open_mods_location = context_menu.addAction(tr("Open Mods Location"));
     QAction* navigate_to_gamedb_entry = context_menu.addAction(tr("Navigate to GameDB entry"));
 
     const bool is_application =
@@ -497,6 +498,7 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
 
     open_texture_dump_location->setVisible(is_application);
     open_texture_load_location->setVisible(is_application);
+    open_mods_location->setVisible(is_application);
 
     navigate_to_gamedb_entry->setVisible(it != compatibility_list.end());
 
@@ -526,6 +528,13 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
             emit OpenFolderRequested(program_id, GameListOpenTarget::TEXTURE_LOAD);
         }
     });
+    connect(open_mods_location, &QAction::triggered, [this, program_id] {
+        if (FileUtil::CreateFullPath(fmt::format("{}mods/{:016X}/",
+                                                 FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                                                 program_id))) {
+            emit OpenFolderRequested(program_id, GameListOpenTarget::MODS);
+        }
+    });
     connect(navigate_to_gamedb_entry, &QAction::triggered, [this, program_id]() {
         emit NavigateToGamedbEntryRequested(program_id, compatibility_list);
     });
diff --git a/src/citra_qt/game_list.h b/src/citra_qt/game_list.h
index ef280ef04..635fbb39b 100644
--- a/src/citra_qt/game_list.h
+++ b/src/citra_qt/game_list.h
@@ -35,7 +35,8 @@ enum class GameListOpenTarget {
     APPLICATION = 2,
     UPDATE_DATA = 3,
     TEXTURE_DUMP = 4,
-    TEXTURE_LOAD = 5
+    TEXTURE_LOAD = 5,
+    MODS = 6,
 };
 
 class GameList : public QWidget {
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index 0a47c7728..cbb29e6d7 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -1141,6 +1141,11 @@ void GMainWindow::OnGameListOpenFolder(u64 data_id, GameListOpenTarget target) {
         path = fmt::format("{}textures/{:016X}/",
                            FileUtil::GetUserPath(FileUtil::UserPath::LoadDir), data_id);
         break;
+    case GameListOpenTarget::MODS:
+        open_target = "Mods";
+        path = fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                           data_id);
+        break;
     default:
         LOG_ERROR(Frontend, "Unexpected target {}", static_cast<int>(target));
         return;

From 53d0c618a03cfa472001d456ddabccf7ab33eba2 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 14:57:32 +0800
Subject: [PATCH 06/16] core/file_sys: Read mods for the original title for
 updates

Updates can override RomFS and ExeFS, therefore we should apply the mods to them as well.
---
 src/core/file_sys/ncch_container.cpp | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index dcc8dd57b..8ddde9e60 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -516,7 +516,7 @@ Loader::ResultStatus NCCHContainer::ApplyCodePatch(std::vector<u8>& code) const
 
     const auto mods_path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id);
+                    ncch_header.program_id & 0x00040000'FFFFFFFF);
     const std::array<PatchLocation, 4> patch_paths{{
         {mods_path + "exefs/code.ips", Patch::ApplyIpsPatch},
         {mods_path + "exefs/code.bps", Patch::ApplyBpsPatch},
@@ -560,7 +560,7 @@ Loader::ResultStatus NCCHContainer::LoadOverrideExeFSSection(const char* name,
 
     const auto mods_path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id);
+                    ncch_header.program_id & 0x00040000'FFFFFFFF);
     std::array<std::string, 2> override_paths{{
         mods_path + "exefs/" + override_name,
         filepath + ".exefsdir/" + override_name,
@@ -625,7 +625,7 @@ Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romf
 
     const auto path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id);
+                    ncch_header.program_id & 0x00040000'FFFFFFFF);
     if (FileUtil::Exists(path + "romfs/") || FileUtil::Exists(path + "romfs_ext/")) {
         romfs_file = std::make_shared<LayeredFS>(std::move(direct_romfs), path + "romfs/",
                                                  path + "romfs_ext/");

From eed9de23369a170e4ab841409edb03cb1ffa1550 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 15:55:35 +0800
Subject: [PATCH 07/16] core/file_sys: Allow exheader replacement to be read
 from mods path

The previous method (filename.exheader) can still be used.
---
 src/core/file_sys/ncch_container.cpp | 18 ++++++++++++++++--
 1 file changed, 16 insertions(+), 2 deletions(-)

diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index 8ddde9e60..11be43c0e 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -304,8 +304,22 @@ Loader::ResultStatus NCCHContainer::Load() {
                 }
             }
 
-            FileUtil::IOFile exheader_override_file{filepath + ".exheader", "rb"};
-            const bool has_exheader_override = read_exheader(exheader_override_file);
+            const auto mods_path =
+                fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
+                            ncch_header.program_id & 0x00040000'FFFFFFFF);
+            std::array<std::string, 2> exheader_override_paths{{
+                mods_path + "exheader.bin",
+                filepath + ".exheader",
+            }};
+
+            bool has_exheader_override = false;
+            for (const auto& path : exheader_override_paths) {
+                FileUtil::IOFile exheader_override_file{path, "rb"};
+                if (read_exheader(exheader_override_file)) {
+                    has_exheader_override = true;
+                    break;
+                }
+            }
             if (has_exheader_override) {
                 if (exheader_header.system_info.jump_id !=
                     exheader_header.arm11_system_local_caps.program_id) {

From 6e0afbaa19d646fb0b6295c88c3656793c471704 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 16:26:33 +0800
Subject: [PATCH 08/16] Fix build

Explicitly use `std::min<std::size_t>`

Added virtual destructor
---
 src/core/file_sys/layered_fs.cpp | 9 +++++----
 src/core/file_sys/layered_fs.h   | 2 +-
 src/core/file_sys/romfs_reader.h | 4 ++++
 3 files changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
index 9a194569a..80719d3fa 100644
--- a/src/core/file_sys/layered_fs.cpp
+++ b/src/core/file_sys/layered_fs.cpp
@@ -515,12 +515,13 @@ std::size_t LayeredFS::ReadFile(std::size_t offset, std::size_t length, u8* buff
         const auto relative_offset = offset - current->first;
         std::size_t to_read{};
         if (current->second->relocation.size > relative_offset) {
-            to_read =
-                std::min(current->second->relocation.size - relative_offset, length - read_size);
+            to_read = std::min<std::size_t>(current->second->relocation.size - relative_offset,
+                                            length - read_size);
         }
         const auto alignment =
-            std::min(Common::AlignUp(current->second->relocation.size, 16) - relative_offset,
-                     length - read_size) -
+            std::min<std::size_t>(Common::AlignUp(current->second->relocation.size, 16) -
+                                      relative_offset,
+                                  length - read_size) -
             to_read;
 
         // Read the file in different ways depending on relocation type
diff --git a/src/core/file_sys/layered_fs.h b/src/core/file_sys/layered_fs.h
index b9dcb831f..4f8844d98 100644
--- a/src/core/file_sys/layered_fs.h
+++ b/src/core/file_sys/layered_fs.h
@@ -42,7 +42,7 @@ class LayeredFS : public RomFSReader {
 public:
     explicit LayeredFS(std::shared_ptr<RomFSReader> romfs, std::string patch_path,
                        std::string patch_ext_path);
-    ~LayeredFS();
+    ~LayeredFS() override;
 
     std::size_t GetSize() const override;
     std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) override;
diff --git a/src/core/file_sys/romfs_reader.h b/src/core/file_sys/romfs_reader.h
index 5ee39015b..df0318c99 100644
--- a/src/core/file_sys/romfs_reader.h
+++ b/src/core/file_sys/romfs_reader.h
@@ -11,6 +11,8 @@ namespace FileSys {
  */
 class RomFSReader {
 public:
+    virtual ~RomFSReader() = default;
+
     virtual std::size_t GetSize() const = 0;
     virtual std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) = 0;
 };
@@ -30,6 +32,8 @@ public:
         : is_encrypted(true), file(std::move(file)), key(key), ctr(ctr), file_offset(file_offset),
           crypto_offset(crypto_offset), data_size(data_size) {}
 
+    ~DirectRomFSReader() override = default;
+
     std::size_t GetSize() const override {
         return data_size;
     }

From 2ec99b83aa4efa75019ccdf1094307c2869fd74b Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 23:45:02 +0800
Subject: [PATCH 09/16] core: Reset archive_manager on shutdown.

This holds the archives which include the SelfNCCH archive which holds the RomFS files. If we don't reset it the LayeredFS class can't get destructed and mods files won't be released.
---
 src/core/core.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/core/core.cpp b/src/core/core.cpp
index ebaee4f87..d217ad003 100644
--- a/src/core/core.cpp
+++ b/src/core/core.cpp
@@ -360,6 +360,7 @@ void System::Shutdown() {
     perf_stats.reset();
     rpc_server.reset();
     cheat_engine.reset();
+    archive_manager.reset();
     service_manager.reset();
     dsp_core.reset();
     cpu_core.reset();

From db18f6c79af679fcd07c75e3355639ae52da78f7 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Fri, 7 Feb 2020 23:53:00 +0800
Subject: [PATCH 10/16] Address review

simplify code
---
 src/core/file_sys/layered_fs.cpp | 12 ++----------
 1 file changed, 2 insertions(+), 10 deletions(-)

diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
index 80719d3fa..65ececd31 100644
--- a/src/core/file_sys/layered_fs.cpp
+++ b/src/core/file_sys/layered_fs.cpp
@@ -306,18 +306,10 @@ void LayeredFS::PrepareBuild(Directory& current) {
 // Implementation from 3dbrew
 u32 CalcHash(const std::string& name, u32 parent_offset) {
     u32 hash = parent_offset ^ 123456789;
-
     std::u16string u16name = Common::UTF8ToUTF16(name);
-    std::vector<u16_le> tmp_buffer(u16name.size());
-    std::transform(u16name.begin(), u16name.end(), tmp_buffer.begin(), [](char16_t character) {
-        return static_cast<u16_le>(static_cast<u16>(character));
-    });
-
-    std::vector<u8> buffer(tmp_buffer.size() * 2);
-    std::memcpy(buffer.data(), tmp_buffer.data(), buffer.size());
-    for (std::size_t i = 0; i < buffer.size(); i += 2) {
+    for (char16_t c : u16name) {
         hash = (hash >> 5) | (hash << 27);
-        hash ^= static_cast<u16>((buffer[i]) | (buffer[i + 1] << 8));
+        hash ^= static_cast<u16>(c);
     }
     return hash;
 }

From 13e2d534e9dc9ec6208df09aa91fb272003844a4 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Sun, 9 Feb 2020 20:59:31 +0800
Subject: [PATCH 11/16] core: Add dump RomFS support

This is added to LayeredFS, then the NCCH container and then the loader interface.
---
 src/core/file_sys/layered_fs.cpp     | 64 ++++++++++++++++++++++++++--
 src/core/file_sys/layered_fs.h       |  8 +++-
 src/core/file_sys/ncch_container.cpp | 22 +++++++++-
 src/core/file_sys/ncch_container.h   | 10 ++++-
 src/core/loader/loader.h             | 18 ++++++++
 src/core/loader/ncch.cpp             | 12 ++++++
 src/core/loader/ncch.h               |  4 ++
 7 files changed, 131 insertions(+), 7 deletions(-)

diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
index 65ececd31..8cfe73846 100644
--- a/src/core/file_sys/layered_fs.cpp
+++ b/src/core/file_sys/layered_fs.cpp
@@ -52,7 +52,7 @@ struct FileMetadata {
 static_assert(sizeof(FileMetadata) == 0x20, "Size of FileMetadata is not correct");
 
 LayeredFS::LayeredFS(std::shared_ptr<RomFSReader> romfs_, std::string patch_path_,
-                     std::string patch_ext_path_)
+                     std::string patch_ext_path_, bool load_relocations)
     : romfs(std::move(romfs_)), patch_path(std::move(patch_path_)),
       patch_ext_path(std::move(patch_ext_path_)) {
 
@@ -64,8 +64,10 @@ LayeredFS::LayeredFS(std::shared_ptr<RomFSReader> romfs_, std::string patch_path
     root.parent = &root;
     LoadDirectory(root, 0);
 
-    LoadRelocations();
-    LoadExtRelocations();
+    if (load_relocations) {
+        LoadRelocations();
+        LoadExtRelocations();
+    }
 
     RebuildMetadata();
 }
@@ -541,4 +543,60 @@ std::size_t LayeredFS::ReadFile(std::size_t offset, std::size_t length, u8* buff
     return read_size;
 }
 
+bool LayeredFS::ExtractDirectory(Directory& current, const std::string& target_path) {
+    if (!FileUtil::CreateFullPath(target_path + current.path)) {
+        LOG_ERROR(Service_FS, "Could not create path {}", target_path + current.path);
+        return false;
+    }
+
+    constexpr std::size_t BufferSize = 0x10000;
+    std::array<u8, BufferSize> buffer;
+    for (const auto& file : current.files) {
+        // Extract file
+        const auto path = target_path + file->path;
+        LOG_INFO(Service_FS, "Extracting {} to {}", file->path, path);
+
+        FileUtil::IOFile target_file(path, "wb");
+        if (!target_file) {
+            LOG_ERROR(Service_FS, "Could not open file {}", path);
+            return false;
+        }
+
+        std::size_t written = 0;
+        while (written < file->relocation.size) {
+            const auto to_read =
+                std::min<std::size_t>(buffer.size(), file->relocation.size - written);
+            if (romfs->ReadFile(file->relocation.original_offset + written, to_read,
+                                buffer.data()) != to_read) {
+                LOG_ERROR(Service_FS, "Could not read from RomFS");
+                return false;
+            }
+
+            if (target_file.WriteBytes(buffer.data(), to_read) != to_read) {
+                LOG_ERROR(Service_FS, "Could not write to file {}", path);
+                return false;
+            }
+
+            written += to_read;
+        }
+    }
+
+    for (const auto& directory : current.directories) {
+        if (!ExtractDirectory(*directory, target_path)) {
+            return false;
+        }
+    }
+
+    return true;
+}
+
+bool LayeredFS::DumpRomFS(const std::string& target_path) {
+    std::string path = target_path;
+    if (path.back() == '/' || path.back() == '\\') {
+        path.erase(path.size() - 1, 1);
+    }
+
+    return ExtractDirectory(root, path);
+}
+
 } // namespace FileSys
diff --git a/src/core/file_sys/layered_fs.h b/src/core/file_sys/layered_fs.h
index 4f8844d98..956eedcfa 100644
--- a/src/core/file_sys/layered_fs.h
+++ b/src/core/file_sys/layered_fs.h
@@ -41,12 +41,14 @@ static_assert(sizeof(RomFSHeader) == 0x28, "Size of RomFSHeader is not correct")
 class LayeredFS : public RomFSReader {
 public:
     explicit LayeredFS(std::shared_ptr<RomFSReader> romfs, std::string patch_path,
-                       std::string patch_ext_path);
+                       std::string patch_ext_path, bool load_relocations = true);
     ~LayeredFS() override;
 
     std::size_t GetSize() const override;
     std::size_t ReadFile(std::size_t offset, std::size_t length, u8* buffer) override;
 
+    bool DumpRomFS(const std::string& target_path);
+
 private:
     struct File;
     struct Directory {
@@ -84,6 +86,10 @@ private:
     void BuildDirectories();
     void BuildFiles();
 
+    // Recursively extract a directory and all its contents to target_path
+    // target_path should be without trailing '/'.
+    bool ExtractDirectory(Directory& current, const std::string& target_path);
+
     void RebuildMetadata();
 
     std::shared_ptr<RomFSReader> romfs;
diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index 11be43c0e..2e549a894 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -597,7 +597,8 @@ Loader::ResultStatus NCCHContainer::LoadOverrideExeFSSection(const char* name,
     return Loader::ResultStatus::ErrorNotUsed;
 }
 
-Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romfs_file) {
+Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romfs_file,
+                                              bool use_layered_fs) {
     Loader::ResultStatus result = Load();
     if (result != Loader::ResultStatus::Success)
         return result;
@@ -640,7 +641,9 @@ Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romf
     const auto path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
                     ncch_header.program_id & 0x00040000'FFFFFFFF);
-    if (FileUtil::Exists(path + "romfs/") || FileUtil::Exists(path + "romfs_ext/")) {
+    if (use_layered_fs &&
+        (FileUtil::Exists(path + "romfs/") || FileUtil::Exists(path + "romfs_ext/"))) {
+
         romfs_file = std::make_shared<LayeredFS>(std::move(direct_romfs), path + "romfs/",
                                                  path + "romfs_ext/");
     } else {
@@ -650,6 +653,21 @@ Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romf
     return Loader::ResultStatus::Success;
 }
 
+Loader::ResultStatus NCCHContainer::DumpRomFS(const std::string& target_path) {
+    std::shared_ptr<RomFSReader> direct_romfs;
+    Loader::ResultStatus result = ReadRomFS(direct_romfs, false);
+    if (result != Loader::ResultStatus::Success)
+        return result;
+
+    std::shared_ptr<LayeredFS> layered_fs =
+        std::make_shared<LayeredFS>(std::move(direct_romfs), "", "", false);
+
+    if (!layered_fs->DumpRomFS(target_path)) {
+        return Loader::ResultStatus::Error;
+    }
+    return Loader::ResultStatus::Success;
+}
+
 Loader::ResultStatus NCCHContainer::ReadOverrideRomFS(std::shared_ptr<RomFSReader>& romfs_file) {
     // Check for RomFS overrides
     std::string split_filepath = filepath + ".romfs";
diff --git a/src/core/file_sys/ncch_container.h b/src/core/file_sys/ncch_container.h
index f06ee8ef6..8deda1fff 100644
--- a/src/core/file_sys/ncch_container.h
+++ b/src/core/file_sys/ncch_container.h
@@ -247,7 +247,15 @@ public:
      * @param size The size of the romfs
      * @return ResultStatus result of function
      */
-    Loader::ResultStatus ReadRomFS(std::shared_ptr<RomFSReader>& romfs_file);
+    Loader::ResultStatus ReadRomFS(std::shared_ptr<RomFSReader>& romfs_file,
+                                   bool use_layered_fs = true);
+
+    /**
+     * Dump the RomFS of the NCCH container to the user folder.
+     * @param target_path target path to dump to
+     * @return ResultStatus result of function.
+     */
+    Loader::ResultStatus DumpRomFS(const std::string& target_path);
 
     /**
      * Get the override RomFS of the NCCH container
diff --git a/src/core/loader/loader.h b/src/core/loader/loader.h
index 20e84c6a9..0414f181c 100644
--- a/src/core/loader/loader.h
+++ b/src/core/loader/loader.h
@@ -186,6 +186,15 @@ public:
         return ResultStatus::ErrorNotImplemented;
     }
 
+    /**
+     * Dump the RomFS of the applciation
+     * @param target_path The target path to dump to
+     * @return ResultStatus result of function
+     */
+    virtual ResultStatus DumpRomFS(const std::string& target_path) {
+        return ResultStatus::ErrorNotImplemented;
+    }
+
     /**
      * Get the update RomFS of the application
      * Since the RomFS can be huge, we return a file reference instead of copying to a buffer
@@ -196,6 +205,15 @@ public:
         return ResultStatus::ErrorNotImplemented;
     }
 
+    /**
+     * Dump the update RomFS of the applciation
+     * @param target_path The target path to dump to
+     * @return ResultStatus result of function
+     */
+    virtual ResultStatus DumpUpdateRomFS(const std::string& target_path) {
+        return ResultStatus::ErrorNotImplemented;
+    }
+
     /**
      * Get the title of the application
      * @param title Reference to store the application title into
diff --git a/src/core/loader/ncch.cpp b/src/core/loader/ncch.cpp
index 2e688e011..21e607ad5 100644
--- a/src/core/loader/ncch.cpp
+++ b/src/core/loader/ncch.cpp
@@ -254,6 +254,18 @@ ResultStatus AppLoader_NCCH::ReadUpdateRomFS(std::shared_ptr<FileSys::RomFSReade
     return ResultStatus::Success;
 }
 
+ResultStatus AppLoader_NCCH::DumpRomFS(const std::string& target_path) {
+    return base_ncch.DumpRomFS(target_path);
+}
+
+ResultStatus AppLoader_NCCH::DumpUpdateRomFS(const std::string& target_path) {
+    u64 program_id;
+    ReadProgramId(program_id);
+    update_ncch.OpenFile(Service::AM::GetTitleContentPath(Service::FS::MediaType::SDMC,
+                                                          program_id | UPDATE_MASK));
+    return update_ncch.DumpRomFS(target_path);
+}
+
 ResultStatus AppLoader_NCCH::ReadTitle(std::string& title) {
     std::vector<u8> data;
     Loader::SMDH smdh;
diff --git a/src/core/loader/ncch.h b/src/core/loader/ncch.h
index 7c86f85d8..041cfddbd 100644
--- a/src/core/loader/ncch.h
+++ b/src/core/loader/ncch.h
@@ -59,6 +59,10 @@ public:
 
     ResultStatus ReadUpdateRomFS(std::shared_ptr<FileSys::RomFSReader>& romfs_file) override;
 
+    ResultStatus DumpRomFS(const std::string& target_path) override;
+
+    ResultStatus DumpUpdateRomFS(const std::string& target_path) override;
+
     ResultStatus ReadTitle(std::string& title) override;
 
 private:

From b87bc5d35157cc70c0284cc521d6d4a9ec4f636b Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Sun, 9 Feb 2020 21:01:56 +0800
Subject: [PATCH 12/16] citra_qt: Add 'Dump RomFS' menu action

A progress dialog will be displayed. However no progress is reported and the user also cannot cancel it.
---
 src/citra_qt/game_list.cpp |  4 ++++
 src/citra_qt/game_list.h   |  1 +
 src/citra_qt/main.cpp      | 41 ++++++++++++++++++++++++++++++++++++++
 src/citra_qt/main.h        |  1 +
 4 files changed, 47 insertions(+)

diff --git a/src/citra_qt/game_list.cpp b/src/citra_qt/game_list.cpp
index 4ba7e99d6..8a5df5172 100644
--- a/src/citra_qt/game_list.cpp
+++ b/src/citra_qt/game_list.cpp
@@ -469,6 +469,7 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
     QAction* open_texture_load_location =
         context_menu.addAction(tr("Open Custom Texture Location"));
     QAction* open_mods_location = context_menu.addAction(tr("Open Mods Location"));
+    QAction* dump_romfs = context_menu.addAction(tr("Dump RomFS"));
     QAction* navigate_to_gamedb_entry = context_menu.addAction(tr("Navigate to GameDB entry"));
 
     const bool is_application =
@@ -499,6 +500,7 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
     open_texture_dump_location->setVisible(is_application);
     open_texture_load_location->setVisible(is_application);
     open_mods_location->setVisible(is_application);
+    dump_romfs->setVisible(is_application);
 
     navigate_to_gamedb_entry->setVisible(it != compatibility_list.end());
 
@@ -535,6 +537,8 @@ void GameList::AddGamePopup(QMenu& context_menu, const QString& path, u64 progra
             emit OpenFolderRequested(program_id, GameListOpenTarget::MODS);
         }
     });
+    connect(dump_romfs, &QAction::triggered,
+            [this, path, program_id] { emit DumpRomFSRequested(path, program_id); });
     connect(navigate_to_gamedb_entry, &QAction::triggered, [this, program_id]() {
         emit NavigateToGamedbEntryRequested(program_id, compatibility_list);
     });
diff --git a/src/citra_qt/game_list.h b/src/citra_qt/game_list.h
index 635fbb39b..334089037 100644
--- a/src/citra_qt/game_list.h
+++ b/src/citra_qt/game_list.h
@@ -82,6 +82,7 @@ signals:
     void OpenFolderRequested(u64 program_id, GameListOpenTarget target);
     void NavigateToGamedbEntryRequested(u64 program_id,
                                         const CompatibilityList& compatibility_list);
+    void DumpRomFSRequested(QString game_path, u64 program_id);
     void OpenDirectory(const QString& directory);
     void AddDirectory();
     void ShowList(bool show);
diff --git a/src/citra_qt/main.cpp b/src/citra_qt/main.cpp
index cbb29e6d7..8534007f6 100644
--- a/src/citra_qt/main.cpp
+++ b/src/citra_qt/main.cpp
@@ -568,6 +568,7 @@ void GMainWindow::ConnectWidgetEvents() {
     connect(game_list, &GameList::OpenFolderRequested, this, &GMainWindow::OnGameListOpenFolder);
     connect(game_list, &GameList::NavigateToGamedbEntryRequested, this,
             &GMainWindow::OnGameListNavigateToGamedbEntry);
+    connect(game_list, &GameList::DumpRomFSRequested, this, &GMainWindow::OnGameListDumpRomFS);
     connect(game_list, &GameList::AddDirectory, this, &GMainWindow::OnGameListAddDirectory);
     connect(game_list_placeholder, &GameListPlaceholder::AddDirectory, this,
             &GMainWindow::OnGameListAddDirectory);
@@ -1177,6 +1178,46 @@ void GMainWindow::OnGameListNavigateToGamedbEntry(u64 program_id,
     QDesktopServices::openUrl(QUrl("https://citra-emu.org/game/" + directory));
 }
 
+void GMainWindow::OnGameListDumpRomFS(QString game_path, u64 program_id) {
+    auto* dialog = new QProgressDialog(tr("Dumping..."), tr("Cancel"), 0, 0, this);
+    dialog->setWindowModality(Qt::WindowModal);
+    dialog->setWindowFlags(dialog->windowFlags() &
+                           ~(Qt::WindowCloseButtonHint | Qt::WindowContextHelpButtonHint));
+    dialog->setCancelButton(nullptr);
+    dialog->setMinimumDuration(0);
+    dialog->setValue(0);
+
+    const auto base_path = fmt::format(
+        "{}romfs/{:016X}", FileUtil::GetUserPath(FileUtil::UserPath::DumpDir), program_id);
+    const auto update_path =
+        fmt::format("{}romfs/{:016X}", FileUtil::GetUserPath(FileUtil::UserPath::DumpDir),
+                    program_id | 0x0004000e00000000);
+    using FutureWatcher = QFutureWatcher<std::pair<Loader::ResultStatus, Loader::ResultStatus>>;
+    auto* future_watcher = new FutureWatcher(this);
+    connect(future_watcher, &FutureWatcher::finished,
+            [this, program_id, dialog, base_path, update_path, future_watcher] {
+                dialog->hide();
+                const auto& [base, update] = future_watcher->result();
+                if (base != Loader::ResultStatus::Success) {
+                    QMessageBox::critical(
+                        this, tr("Citra"),
+                        tr("Could not dump base RomFS.\nRefer to the log for details."));
+                    return;
+                }
+                QDesktopServices::openUrl(QUrl::fromLocalFile(QString::fromStdString(base_path)));
+                if (update == Loader::ResultStatus::Success) {
+                    QDesktopServices::openUrl(
+                        QUrl::fromLocalFile(QString::fromStdString(update_path)));
+                }
+            });
+
+    auto future = QtConcurrent::run([game_path, base_path, update_path] {
+        std::unique_ptr<Loader::AppLoader> loader = Loader::GetLoader(game_path.toStdString());
+        return std::make_pair(loader->DumpRomFS(base_path), loader->DumpUpdateRomFS(update_path));
+    });
+    future_watcher->setFuture(future);
+}
+
 void GMainWindow::OnGameListOpenDirectory(const QString& directory) {
     QString path;
     if (directory == QStringLiteral("INSTALLED")) {
diff --git a/src/citra_qt/main.h b/src/citra_qt/main.h
index 91d7eed1b..75a1bbb3d 100644
--- a/src/citra_qt/main.h
+++ b/src/citra_qt/main.h
@@ -169,6 +169,7 @@ private slots:
     void OnGameListOpenFolder(u64 program_id, GameListOpenTarget target);
     void OnGameListNavigateToGamedbEntry(u64 program_id,
                                          const CompatibilityList& compatibility_list);
+    void OnGameListDumpRomFS(QString game_path, u64 program_id);
     void OnGameListOpenDirectory(const QString& directory);
     void OnGameListAddDirectory();
     void OnGameListShowList(bool show);

From d9ae4c332d11466351dc231531bf2a4f424ae8c1 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Sun, 9 Feb 2020 21:48:42 +0800
Subject: [PATCH 13/16] layered_fs: Do not open all replacement files on load

Instead open them when we want to read them. This is because the standard library has a limit on the number of opened files.
---
 src/core/file_sys/layered_fs.cpp | 23 ++++++++++++-----------
 1 file changed, 12 insertions(+), 11 deletions(-)

diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
index 8cfe73846..a77ab38f1 100644
--- a/src/core/file_sys/layered_fs.cpp
+++ b/src/core/file_sys/layered_fs.cpp
@@ -18,7 +18,7 @@ namespace FileSys {
 struct FileRelocationInfo {
     int type;                      // 0 - none, 1 - replaced / created, 2 - patched, 3 - removed
     u64 original_offset;           // Type 0. Offset is absolute
-    FileUtil::IOFile replace_file; // Type 1
+    std::string replace_file_path; // Type 1
     std::vector<u8> patched_file;  // Type 2
     u64 size;                      // Relocated file size
 };
@@ -175,14 +175,9 @@ void LayeredFS::LoadRelocations() {
         }
 
         auto* file = file_path_map.at(path);
-        file->relocation.replace_file = FileUtil::IOFile(directory + virtual_name, "rb");
-        if (file->relocation.replace_file) {
-            file->relocation.type = 1;
-            file->relocation.size = file->relocation.replace_file.GetSize();
-            LOG_INFO(Service_FS, "LayeredFS replacement file in use for {}", path);
-        } else {
-            LOG_ERROR(Service_FS, "Could not open replacement file for {}", path);
-        }
+        file->relocation.type = 1;
+        file->relocation.replace_file_path = directory + virtual_name;
+        LOG_INFO(Service_FS, "LayeredFS replacement file in use for {}", path);
         return true;
     };
 
@@ -524,8 +519,14 @@ std::size_t LayeredFS::ReadFile(std::size_t offset, std::size_t length, u8* buff
             romfs->ReadFile(relocation.original_offset + relative_offset, to_read,
                             buffer + read_size);
         } else if (relocation.type == 1) { // replace
-            relocation.replace_file.Seek(relative_offset, SEEK_SET);
-            relocation.replace_file.ReadBytes(buffer + read_size, to_read);
+            FileUtil::IOFile replace_file(relocation.replace_file_path, "rb");
+            if (replace_file) {
+                replace_file.Seek(relative_offset, SEEK_SET);
+                replace_file.ReadBytes(buffer + read_size, to_read);
+            } else {
+                LOG_ERROR(Service_FS, "Could not open replacement file for {}",
+                          current->second->path);
+            }
         } else if (relocation.type == 2) { // patch
             std::memcpy(buffer + read_size, relocation.patched_file.data() + relative_offset,
                         to_read);

From b81c9bd73853f281b2f223a4469fa9dfd264d380 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Mon, 10 Feb 2020 07:41:31 +0800
Subject: [PATCH 14/16] fix clang format

---
 src/core/loader/ncch.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/core/loader/ncch.cpp b/src/core/loader/ncch.cpp
index 21e607ad5..1a966da5e 100644
--- a/src/core/loader/ncch.cpp
+++ b/src/core/loader/ncch.cpp
@@ -261,8 +261,8 @@ ResultStatus AppLoader_NCCH::DumpRomFS(const std::string& target_path) {
 ResultStatus AppLoader_NCCH::DumpUpdateRomFS(const std::string& target_path) {
     u64 program_id;
     ReadProgramId(program_id);
-    update_ncch.OpenFile(Service::AM::GetTitleContentPath(Service::FS::MediaType::SDMC,
-                                                          program_id | UPDATE_MASK));
+    update_ncch.OpenFile(
+        Service::AM::GetTitleContentPath(Service::FS::MediaType::SDMC, program_id | UPDATE_MASK));
     return update_ncch.DumpRomFS(target_path);
 }
 

From 4273b967b5a0b07df18ebcc0131eb11dda497bc8 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Tue, 11 Feb 2020 14:03:07 +0800
Subject: [PATCH 15/16] core/file_sys: Do not apply the same mods to DLCs

Now you can apply separate mods to DLCs and mods for the original title won't be applied.
---
 src/core/file_sys/ncch_container.cpp | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/src/core/file_sys/ncch_container.cpp b/src/core/file_sys/ncch_container.cpp
index 2e549a894..81525786f 100644
--- a/src/core/file_sys/ncch_container.cpp
+++ b/src/core/file_sys/ncch_container.cpp
@@ -26,6 +26,14 @@ namespace FileSys {
 static const int kMaxSections = 8;   ///< Maximum number of sections (files) in an ExeFs
 static const int kBlockSize = 0x200; ///< Size of ExeFS blocks (in bytes)
 
+u64 GetModId(u64 program_id) {
+    constexpr u64 UPDATE_MASK = 0x0000000e'00000000;
+    if ((program_id & 0x000000ff'00000000) == UPDATE_MASK) { // Apply the mods to updates
+        return program_id & ~UPDATE_MASK;
+    }
+    return program_id;
+}
+
 /**
  * Get the decompressed size of an LZSS compressed ExeFS file
  * @param buffer Buffer of compressed file
@@ -306,7 +314,7 @@ Loader::ResultStatus NCCHContainer::Load() {
 
             const auto mods_path =
                 fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                            ncch_header.program_id & 0x00040000'FFFFFFFF);
+                            GetModId(ncch_header.program_id));
             std::array<std::string, 2> exheader_override_paths{{
                 mods_path + "exheader.bin",
                 filepath + ".exheader",
@@ -530,7 +538,7 @@ Loader::ResultStatus NCCHContainer::ApplyCodePatch(std::vector<u8>& code) const
 
     const auto mods_path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id & 0x00040000'FFFFFFFF);
+                    GetModId(ncch_header.program_id));
     const std::array<PatchLocation, 4> patch_paths{{
         {mods_path + "exefs/code.ips", Patch::ApplyIpsPatch},
         {mods_path + "exefs/code.bps", Patch::ApplyBpsPatch},
@@ -574,7 +582,7 @@ Loader::ResultStatus NCCHContainer::LoadOverrideExeFSSection(const char* name,
 
     const auto mods_path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id & 0x00040000'FFFFFFFF);
+                    GetModId(ncch_header.program_id));
     std::array<std::string, 2> override_paths{{
         mods_path + "exefs/" + override_name,
         filepath + ".exefsdir/" + override_name,
@@ -640,7 +648,7 @@ Loader::ResultStatus NCCHContainer::ReadRomFS(std::shared_ptr<RomFSReader>& romf
 
     const auto path =
         fmt::format("{}mods/{:016X}/", FileUtil::GetUserPath(FileUtil::UserPath::LoadDir),
-                    ncch_header.program_id & 0x00040000'FFFFFFFF);
+                    GetModId(ncch_header.program_id));
     if (use_layered_fs &&
         (FileUtil::Exists(path + "romfs/") || FileUtil::Exists(path + "romfs_ext/"))) {
 

From 8eacfceb6a14a9862eae8e82fbfc06a0a8d7fad3 Mon Sep 17 00:00:00 2001
From: zhupengfei <zhupf321@gmail.com>
Date: Sun, 23 Feb 2020 15:22:41 +0800
Subject: [PATCH 16/16] layered_fs: Fix missing file size update

This was a silly typo from a previous change.
---
 src/core/file_sys/layered_fs.cpp | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/core/file_sys/layered_fs.cpp b/src/core/file_sys/layered_fs.cpp
index a77ab38f1..9d5fbf7c2 100644
--- a/src/core/file_sys/layered_fs.cpp
+++ b/src/core/file_sys/layered_fs.cpp
@@ -177,6 +177,7 @@ void LayeredFS::LoadRelocations() {
         auto* file = file_path_map.at(path);
         file->relocation.type = 1;
         file->relocation.replace_file_path = directory + virtual_name;
+        file->relocation.size = FileUtil::GetSize(directory + virtual_name);
         LOG_INFO(Service_FS, "LayeredFS replacement file in use for {}", path);
         return true;
     };