diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index c9027c9..3dc361f 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -32,8 +32,8 @@ jobs:
 
       - name: Build
         shell: pwsh
-        run: python build_native.py
+        run: python scripts/build.py
 
       - name: Smoke tests
         shell: pwsh
-        run: python core\native\tests\native_smoke.py
+        run: python proto/tests/native_smoke.py
diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index bbb6a10..9efc6f8 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -37,24 +37,24 @@ jobs:
       - name: Build and test
         shell: pwsh
         run: |
-          python build_native.py
+          python scripts/build.py
           if ($LASTEXITCODE -ne 0) { throw 'Native build failed' }
-          python core\native\tests\native_smoke.py
+          python proto/tests/native_smoke.py
           if ($LASTEXITCODE -ne 0) { throw 'Smoke tests failed' }
 
       - name: Package flat distribution
         shell: pwsh
         run: |
           $files = @(
-            'dist/binary/QuickFileCopy.exe',
-            'dist/binary/QuickFileCopy_cli.exe',
-            'dist/binary/WebView2Loader.dll',
-            'dist/documents/readme.txt',
-            'dist/documents/readme_jp.txt',
-            'dist/documents/history.txt',
-            'dist/documents/history_jp.txt',
-            'dist/documents/LICENSE.txt',
-            'dist/documents/LICENSE_jp.txt'
+            'dist/QuickFileCopy.exe',
+            'dist/QuickFileCopy_cli.exe',
+            'dist/WebView2Loader.dll',
+            'docs/distribution/readme.txt',
+            'docs/distribution/readme_jp.txt',
+            'docs/distribution/history.txt',
+            'docs/distribution/history_jp.txt',
+            'docs/distribution/LICENSE.txt',
+            'docs/distribution/LICENSE_jp.txt'
           )
           foreach ($file in $files) {
             if (!(Test-Path -LiteralPath $file)) { throw "Missing distribution file: $file" }
@@ -64,12 +64,34 @@ jobs:
           foreach ($file in $files) { Copy-Item -LiteralPath $file -Destination $staging -Force }
           Compress-Archive -Path (Join-Path $staging '*') -DestinationPath 'QuickFileCopy-binary.zip' -Force
 
+      - name: Generate SHA-256 checksums
+        shell: pwsh
+        run: |
+          $checksumFile = Join-Path $env:GITHUB_WORKSPACE 'SHA256SUMS.txt'
+          $lines = @()
+          $zipPath = Join-Path $env:GITHUB_WORKSPACE 'QuickFileCopy-binary.zip'
+          $zipHash = (Get-FileHash -Algorithm SHA256 -Path $zipPath).Hash.ToUpper()
+          $lines += "$zipHash  QuickFileCopy-binary.zip"
+          $lines += ""
+          $lines += "# Binaries inside archive:"
+          $binFiles = @('dist/QuickFileCopy.exe', 'dist/QuickFileCopy_cli.exe', 'dist/WebView2Loader.dll')
+          foreach ($f in $binFiles) {
+            if (Test-Path -LiteralPath $f) {
+              $h = (Get-FileHash -Algorithm SHA256 -Path $f).Hash.ToUpper()
+              $name = Split-Path -Leaf $f
+              $lines += "$h  $name"
+            }
+          }
+          $lines | Set-Content -Path $checksumFile -Encoding utf8
+
       - name: Upload release asset
         uses: softprops/action-gh-release@v2
         with:
           tag_name: ${{ github.event_name == 'workflow_dispatch' && inputs.tag || github.ref_name }}
           name: ${{ github.event_name == 'workflow_dispatch' && inputs.tag || github.ref_name }}
-          files: QuickFileCopy-binary.zip
+          files: |
+            QuickFileCopy-binary.zip
+            SHA256SUMS.txt
           overwrite_files: true
           generate_release_notes: true
           body: |
diff --git a/.gitignore b/.gitignore
index 61ce5e7..2244083 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,4 +1,14 @@
-# Python and test caches
+# Build output & intermediate files
+build/
+dist/*
+!dist/.gitkeep
+*.o
+*.exe
+*.dll
+*.log
+*_debug.log
+
+# Python & virtual environments
 __pycache__/
 *.py[cod]
 *$py.class
@@ -9,34 +19,16 @@ env/
 *.egg-info/
 .env
 
-# Editors and local tools
+# Editors & local tools
 .vscode/
 .idea/
 .claude/
+CODEX_PROJECT_NOTE.txt
 
-# C++ and CMake outputs
-build/
-core/native/*.dll
-core/native/*.o
-core/native/resources/QuickFileCopy.html
-
-# Distribution binaries are generated; distribution documents are retained.
-dist/binary/*
-!dist/binary/.gitkeep
-dist/*.zip
-
-# Benchmark data generated on local machines
-python/benchmark/testdata/
-python/benchmark/**/results/*.json
-
-# Prototype build outputs
-python/prototype/*.dist/
-python/prototype/*.build/
-python/prototype/*.onefile-build/
-
-# Reference repositories and logs
-reference/
-*.log
+# Benchmark & test data
+proto/benchmark/testdata/
+proto/benchmark/**/results/*.json
+proto/prototype/*.dist/
+proto/prototype/*.build/
+proto/prototype/*.onefile-build/
 *.dat
-*_debug.log
-CODEX_PROJECT_NOTE.txt
diff --git a/README.md b/README.md
index 476b73b..f79de50 100644
--- a/README.md
+++ b/README.md
@@ -42,6 +42,14 @@ Extract every file into the same folder and run `QuickFileCopy.exe`.
 - `history.txt` / `history_jp.txt` - change log
 - `LICENSE.txt` / `LICENSE_jp.txt` - license files
 
+### Integrity verification (SHA-256)
+
+Official SHA-256 checksums for the distribution ZIP and binaries are automatically computed during the CI (GitHub Actions) build and published as `SHA256SUMS.txt` on each release page. Verify the downloaded package with PowerShell:
+
+```powershell
+Get-FileHash .\QuickFileCopy-binary.zip -Algorithm SHA256
+```
+
 The GUI HTML is embedded in `QuickFileCopy.exe`; an external `index.html` is not required.
 
 ## GUI usage
@@ -57,9 +65,9 @@ Complete-preservation modes launch a separate elevated worker through UAC. The m
 ## CLI usage
 
 ```powershell
-.\dist\binary\QuickFileCopy_cli.exe --help
-.\dist\binary\QuickFileCopy_cli.exe copy C:\Source D:\Backup --contents --policy newer
-.\dist\binary\QuickFileCopy_cli.exe copy C:\Source D:\Backup --folder --policy overwrite --verify
+.\dist\QuickFileCopy_cli.exe --help
+.\dist\QuickFileCopy_cli.exe copy C:\Source D:\Backup --contents --policy newer
+.\dist\QuickFileCopy_cli.exe copy C:\Source D:\Backup --folder --policy overwrite --verify
 ```
 
 ## Build
@@ -73,33 +81,37 @@ Requirements:
 
 ```powershell
 winget install --id BrechtSanders.WinLibs.MCF.UCRT --exact --source winget
-build.bat
+scripts\build.bat
 ```
 
 The default WebView2 SDK root is `C:\tools\webview2\build\native`. Override it with `WEBVIEW2_ROOT`, `WEBVIEW2_INCLUDE`, or `WEBVIEW2_LOADER`.
 
-Build outputs are written to `dist\binary`. Run the smoke tests after building:
+Build outputs are written to `dist/`. Run the smoke tests after building:
 
 ```powershell
-python python\tests\native_smoke.py
+python proto\tests\native_smoke.py
 ```
 
-Detailed specifications and build notes are in [`document/`](document/).
+Detailed specifications and build notes are in [`docs/`](docs/).
 
 ## Project layout
 
 ```text
-core/native/       C++ engine, GUI host, CLI, and resources
-python/prototype/  archived Python/PySide6 prototype
-python/tests/      native CLI smoke and benchmark runners
-python/benchmark/  historical Python prototype measurements
-templates/         self-contained WebView2 development UI
-static/            reserved CSS/JS/image source area
-assets/            icon sources and future public screenshots
-document/          specification, environment, and version information
-plans/             dated implementation plans and results
-dist/binary/       generated binaries, excluded from source control
-dist/documents/    user-facing distribution documents
+QuickFileCopy/
+├── src/
+│   ├── app/              GUI host & Windows resources (main_gui.cpp, .rc, .ico, resource.h)
+│   ├── cli/              CLI entry point (main_cli.cpp)
+│   ├── engine/           Copy engine and qfc/ header (copy_engine.cpp, qfc/copy_engine.h)
+│   └── ui/               UI source files (index.html, css/, js/, img/)
+├── proto/
+│   ├── prototype/        archived Python/PySide6 prototype
+│   ├── tests/            native CLI smoke and benchmark runners
+│   └── benchmark/        historical Python prototype measurements
+├── scripts/              build.py, build.bat, bundle_html.py
+├── docs/                 specification, environment, and version information
+│   └── distribution/     user-facing distribution documents
+├── dist/                 generated binaries, excluded from source control (except .gitkeep)
+└── .github/workflows/    CI and release workflows
 ```
 
 ## License and disclaimer
diff --git a/README_jp.md b/README_jp.md
index e8f3c83..6c42c7a 100644
--- a/README_jp.md
+++ b/README_jp.md
@@ -42,6 +42,14 @@ GUIと文書は日本語／Englishに対応し、QDB形式の言語ボタンで
 - `history.txt` / `history_jp.txt` - 更新履歴
 - `LICENSE.txt` / `LICENSE_jp.txt` - ライセンス
 
+### 完全性検証 (SHA-256)
+
+配布用 ZIP および各バイナリの公式 SHA-256 ハッシュ値は、CI (GitHub Actions) ビルド時に自動計算され、各リリースページに `SHA256SUMS.txt` として添付・公開されています。PowerShell でダウンロードファイルの完全性を確認できます:
+
+```powershell
+Get-FileHash .\QuickFileCopy-binary.zip -Algorithm SHA256
+```
+
 GUIのHTMLは`QuickFileCopy.exe`へ埋め込まれるため、外部の`index.html`は不要です。
 
 ## GUIの使い方
@@ -57,9 +65,9 @@ GUIのHTMLは`QuickFileCopy.exe`へ埋め込まれるため、外部の`index.ht
 ## CLIの使い方
 
 ```powershell
-.\dist\binary\QuickFileCopy_cli.exe --help
-.\dist\binary\QuickFileCopy_cli.exe copy C:\Source D:\Backup --contents --policy newer
-.\dist\binary\QuickFileCopy_cli.exe copy C:\Source D:\Backup --folder --policy overwrite --verify
+.\dist\QuickFileCopy_cli.exe --help
+.\dist\QuickFileCopy_cli.exe copy C:\Source D:\Backup --contents --policy newer
+.\dist\QuickFileCopy_cli.exe copy C:\Source D:\Backup --folder --policy overwrite --verify
 ```
 
 ## ビルド
@@ -73,33 +81,37 @@ GUIのHTMLは`QuickFileCopy.exe`へ埋め込まれるため、外部の`index.ht
 
 ```powershell
 winget install --id BrechtSanders.WinLibs.MCF.UCRT --exact --source winget
-build.bat
+scripts\build.bat
 ```
 
 WebView2 SDKの既定ルートは`C:\tools\webview2\build\native`です。別の場所を使う場合は`WEBVIEW2_ROOT`、`WEBVIEW2_INCLUDE`、`WEBVIEW2_LOADER`で指定できます。
 
-成果物は`dist\binary`へ出力されます。ビルド後のスモークテスト:
+成果物は`dist/`へ出力されます。ビルド後のスモークテスト:
 
 ```powershell
-python python\tests\native_smoke.py
+python proto\tests\native_smoke.py
 ```
 
-詳しい仕様とビルド情報は[`document/`](document/)にあります。
+詳しい仕様とビルド情報は[`docs/`](docs/)にあります。
 
 ## フォルダ構成
 
 ```text
-core/native/       C++エンジン、GUIホスト、CLI、リソース
-python/prototype/  旧Python/PySide6プロトタイプ
-python/tests/      ネイティブCLIのスモークとベンチマーク
-python/benchmark/  旧Python試作の計測記録
-templates/         自己完結WebView2開発用UI
-static/            CSS/JS/画像を分離する場合の配置先
-assets/            アイコン原本と今後の公開用スクリーンショット
-document/          仕様、開発環境、バージョン情報
-plans/             日付付きの計画書と実施結果
-dist/binary/       生成バイナリ（ソース管理対象外）
-dist/documents/    配布用ユーザー文書
+QuickFileCopy/
+├── src/
+│   ├── app/              GUIホスト & Windowsリソース（main_gui.cpp, .rc, .ico, resource.h）
+│   ├── cli/              CLIエントリーポイント（main_cli.cpp）
+│   ├── engine/           コピーエンジンおよびqfc/ヘッダー（copy_engine.cpp, qfc/copy_engine.h）
+│   └── ui/               UIソース（index.html, css/, js/, img/）
+├── proto/
+│   ├── prototype/        旧Python/PySide6プロトタイプ
+│   ├── tests/            ネイティブCLIのスモークとベンチマーク
+│   └── benchmark/        旧Python試作の計測記録
+├── scripts/              build.py, build.bat, bundle_html.py
+├── docs/                 仕様、開発環境、バージョン情報
+│   └── distribution/     配布用ユーザー文書
+├── dist/                 生成バイナリ（ソース管理対象外、.gitkeepのみ保持）
+└── .github/workflows/    CI / Release ワークフロー
 ```
 
 ## ライセンスと免責
diff --git a/build.bat b/build.bat
deleted file mode 100644
index 8cf9927..0000000
--- a/build.bat
+++ /dev/null
@@ -1,5 +0,0 @@
-@echo off
-setlocal
-cd /d "%~dp0"
-python build_native.py
-exit /b %ERRORLEVEL%
diff --git a/core/native/CMakeLists.txt b/core/native/CMakeLists.txt
deleted file mode 100644
index 53d3434..0000000
--- a/core/native/CMakeLists.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-cmake_minimum_required(VERSION 3.24)
-project(QuickFileCopyNative VERSION 1.0.0 LANGUAGES CXX RC)
-
-set(CMAKE_CXX_STANDARD 20)
-set(CMAKE_CXX_STANDARD_REQUIRED ON)
-set(CMAKE_CXX_EXTENSIONS OFF)
-
-if(NOT WIN32)
-  message(FATAL_ERROR "QuickFileCopy native is Windows-only")
-endif()
-
-set(WEBVIEW2_INCLUDE "C:/tools/webview2/build/native/include" CACHE PATH "WebView2 SDK include directory")
-set(QFC_ICON_PATH "${CMAKE_CURRENT_SOURCE_DIR}/resources/QuickFileCopy.ico")
-set(QFC_HTML_PATH "${CMAKE_CURRENT_SOURCE_DIR}/resources/QuickFileCopy.html")
-configure_file(
-  resources/QuickFileCopy.rc.in
-  "${CMAKE_CURRENT_BINARY_DIR}/QuickFileCopy.rc"
-  @ONLY
-)
-
-add_library(qfc_core STATIC src/copy_engine.cpp)
-target_include_directories(qfc_core PUBLIC include)
-target_compile_definitions(qfc_core PUBLIC UNICODE _UNICODE WINVER=0x0A00 _WIN32_WINNT=0x0A00)
-
-add_executable(QuickFileCopy_cli src/main_cli.cpp)
-target_link_libraries(QuickFileCopy_cli PRIVATE qfc_core kernel32 advapi32 bcrypt)
-if(MINGW)
-  target_link_options(QuickFileCopy_cli PRIVATE -municode)
-endif()
-
-add_executable(QuickFileCopy WIN32
-  src/webview_main.cpp
-  "${CMAKE_CURRENT_BINARY_DIR}/QuickFileCopy.rc"
-)
-target_include_directories(QuickFileCopy PRIVATE "${WEBVIEW2_INCLUDE}" resources)
-target_compile_definitions(QuickFileCopy PRIVATE UNICODE _UNICODE WINVER=0x0A00 _WIN32_WINNT=0x0A00)
-target_link_libraries(QuickFileCopy PRIVATE qfc_core kernel32 user32 dwmapi ole32 uuid shell32 advapi32 bcrypt)
-
-if(MINGW)
-  foreach(target QuickFileCopy_cli QuickFileCopy)
-    target_compile_options(${target} PRIVATE -O3 -ffunction-sections -fdata-sections)
-    target_link_options(${target} PRIVATE -static -static-libgcc -static-libstdc++ -Wl,--gc-sections)
-  endforeach()
-endif()
diff --git a/core/native/README.md b/core/native/README.md
deleted file mode 100644
index cf247b0..0000000
--- a/core/native/README.md
+++ /dev/null
@@ -1,32 +0,0 @@
-# QuickFileCopy native implementation
-
-This directory contains the production C++20 implementation. It does not link to or embed the archived Python prototype.
-
-## Files
-
-```text
-include/qfc/copy_engine.h  public copy-engine API
-src/copy_engine.cpp        scanner, queue, copy paths, verification, metadata
-src/webview_main.cpp       Win32 window, WebView2 host, UAC worker, WebMessage
-src/main_cli.cpp            command-line application
-resources/                  resource script, VERSIONINFO, generated embedded HTML
-```
-
-Python smoke tests live in `python/tests/`. The standard build entry point is the repository-root `build.bat` or `build_native.py`.
-
-```powershell
-build.bat
-python python\tests\native_smoke.py
-```
-
-Outputs:
-
-```text
-dist/binary/QuickFileCopy.exe
-dist/binary/QuickFileCopy_cli.exe
-dist/binary/WebView2Loader.dll
-```
-
-The GUI HTML is generated from `templates/index.html` and embedded into the executable. It is not a separate runtime file.
-
-See `document/spec.md` for behavior and `document/environment.md` for the complete build environment.
diff --git a/core/native/resources/QuickFileCopy.rc.in b/core/native/resources/QuickFileCopy.rc.in
deleted file mode 100644
index 60be5ce..0000000
--- a/core/native/resources/QuickFileCopy.rc.in
+++ /dev/null
@@ -1,33 +0,0 @@
-#include "@CMAKE_CURRENT_SOURCE_DIR@/resources/resource.h"
-
-IDI_APP_ICON ICON "@QFC_ICON_PATH@"
-IDR_APP_HTML RCDATA "@QFC_HTML_PATH@"
-
-1 VERSIONINFO
- FILEVERSION 1,0,0,0
- PRODUCTVERSION 1,0,0,0
- FILEFLAGSMASK 0x3fL
- FILEFLAGS 0x0L
- FILEOS 0x40004L
- FILETYPE 0x1L
- FILESUBTYPE 0x0L
-BEGIN
-  BLOCK "StringFileInfo"
-  BEGIN
-    BLOCK "041104B0"
-    BEGIN
-      VALUE "CompanyName", "QuickFileCopy Project\0"
-      VALUE "FileDescription", "QuickFileCopy - Native High-Speed File Copy\0"
-      VALUE "FileVersion", "1.0.0\0"
-      VALUE "InternalName", "QuickFileCopy\0"
-      VALUE "LegalCopyright", "Copyright (C) 2026 QuickFileCopy contributors\0"
-      VALUE "OriginalFilename", "QuickFileCopy.exe\0"
-      VALUE "ProductName", "QuickFileCopy\0"
-      VALUE "ProductVersion", "1.0.0\0"
-    END
-  END
-  BLOCK "VarFileInfo"
-  BEGIN
-    VALUE "Translation", 0x0411, 1200
-  END
-END
diff --git a/dist/binary/.gitkeep b/dist/.gitkeep
similarity index 100%
rename from dist/binary/.gitkeep
rename to dist/.gitkeep
diff --git a/document/about.md b/docs/about.md
similarity index 100%
rename from document/about.md
rename to docs/about.md
diff --git a/document/about_jp.md b/docs/about_jp.md
similarity index 100%
rename from document/about_jp.md
rename to docs/about_jp.md
diff --git a/dist/documents/LICENSE.txt b/docs/distribution/LICENSE.txt
similarity index 100%
rename from dist/documents/LICENSE.txt
rename to docs/distribution/LICENSE.txt
diff --git a/dist/documents/LICENSE_jp.txt b/docs/distribution/LICENSE_jp.txt
similarity index 100%
rename from dist/documents/LICENSE_jp.txt
rename to docs/distribution/LICENSE_jp.txt
diff --git a/dist/documents/history.txt b/docs/distribution/history.txt
similarity index 100%
rename from dist/documents/history.txt
rename to docs/distribution/history.txt
diff --git a/dist/documents/history_jp.txt b/docs/distribution/history_jp.txt
similarity index 100%
rename from dist/documents/history_jp.txt
rename to docs/distribution/history_jp.txt
diff --git a/dist/documents/readme.txt b/docs/distribution/readme.txt
similarity index 88%
rename from dist/documents/readme.txt
rename to docs/distribution/readme.txt
index 950e011..84727cc 100644
--- a/dist/documents/readme.txt
+++ b/docs/distribution/readme.txt
@@ -43,10 +43,12 @@ Distribution files
 - history.txt / history_jp.txt - change log
 - LICENSE.txt / LICENSE_jp.txt - MIT License files
 
-SHA-256
--------
-DD5CB93CF84CD6FE5D0DF78DC1A640B3CF97EF4E153989CC8F39A7EF681651E7  QuickFileCopy.exe
-5CAE1046B51B5D60EB929561294E3E2F526C62CAA97A828BA9B326F693E08843  QuickFileCopy_cli.exe
+Integrity verification (SHA-256)
+--------------------------------
+Official SHA-256 checksums are automatically generated by the CI build and
+published as SHA256SUMS.txt on each GitHub Release page. Verify with PowerShell:
+  Get-FileHash .\QuickFileCopy-binary.zip -Algorithm SHA256
+
 
 License
 -------
diff --git a/dist/documents/readme_jp.txt b/docs/distribution/readme_jp.txt
similarity index 86%
rename from dist/documents/readme_jp.txt
rename to docs/distribution/readme_jp.txt
index f728cf8..ebc00b9 100644
--- a/dist/documents/readme_jp.txt
+++ b/docs/distribution/readme_jp.txt
@@ -43,10 +43,12 @@ QuickFileCopy_cli.exe --help
 - history.txt / history_jp.txt - 更新履歴
 - LICENSE.txt / LICENSE_jp.txt - MIT License
 
-SHA-256
--------
-DD5CB93CF84CD6FE5D0DF78DC1A640B3CF97EF4E153989CC8F39A7EF681651E7  QuickFileCopy.exe
-5CAE1046B51B5D60EB929561294E3E2F526C62CAA97A828BA9B326F693E08843  QuickFileCopy_cli.exe
+完全性検証（SHA-256）
+---------------------
+配布用ZIPおよびバイナリの公式SHA-256ハッシュ値はCIビルド時に自動計算され、
+GitHub Releasesの各リリースに SHA256SUMS.txt として添付・公開されています。
+PowerShellでダウンロードファイルの整合性を確認できます:
+  Get-FileHash .\QuickFileCopy-binary.zip -Algorithm SHA256
 
 ライセンス
 ----------
diff --git a/document/environment.md b/docs/environment.md
similarity index 100%
rename from document/environment.md
rename to docs/environment.md
diff --git a/document/environment_jp.md b/docs/environment_jp.md
similarity index 100%
rename from document/environment_jp.md
rename to docs/environment_jp.md
diff --git a/document/spec.md b/docs/spec.md
similarity index 100%
rename from document/spec.md
rename to docs/spec.md
diff --git a/document/spec_jp.md b/docs/spec_jp.md
similarity index 100%
rename from document/spec_jp.md
rename to docs/spec_jp.md
diff --git a/python/benchmark/README.md b/proto/benchmark/README.md
similarity index 100%
rename from python/benchmark/README.md
rename to proto/benchmark/README.md
diff --git a/python/benchmark/generate_dataset.py b/proto/benchmark/generate_dataset.py
similarity index 100%
rename from python/benchmark/generate_dataset.py
rename to proto/benchmark/generate_dataset.py
diff --git a/python/benchmark/results/fastcopy_comparison.md b/proto/benchmark/results/fastcopy_comparison.md
similarity index 100%
rename from python/benchmark/results/fastcopy_comparison.md
rename to proto/benchmark/results/fastcopy_comparison.md
diff --git a/python/benchmark/results/final_comparison.md b/proto/benchmark/results/final_comparison.md
similarity index 100%
rename from python/benchmark/results/final_comparison.md
rename to proto/benchmark/results/final_comparison.md
diff --git a/python/benchmark/results/large_files_benchmark.md b/proto/benchmark/results/large_files_benchmark.md
similarity index 100%
rename from python/benchmark/results/large_files_benchmark.md
rename to proto/benchmark/results/large_files_benchmark.md
diff --git a/python/benchmark/results/small_files_benchmark.md b/proto/benchmark/results/small_files_benchmark.md
similarity index 100%
rename from python/benchmark/results/small_files_benchmark.md
rename to proto/benchmark/results/small_files_benchmark.md
diff --git a/python/benchmark/run_benchmark.py b/proto/benchmark/run_benchmark.py
similarity index 100%
rename from python/benchmark/run_benchmark.py
rename to proto/benchmark/run_benchmark.py
diff --git a/python/prototype/build_exe.ps1 b/proto/prototype/build_exe.ps1
similarity index 100%
rename from python/prototype/build_exe.ps1
rename to proto/prototype/build_exe.ps1
diff --git a/python/prototype/nuitka-crash-report.xml b/proto/prototype/nuitka-crash-report.xml
similarity index 100%
rename from python/prototype/nuitka-crash-report.xml
rename to proto/prototype/nuitka-crash-report.xml
diff --git a/python/prototype/pyproject.toml b/proto/prototype/pyproject.toml
similarity index 100%
rename from python/prototype/pyproject.toml
rename to proto/prototype/pyproject.toml
diff --git a/python/prototype/requirements.txt b/proto/prototype/requirements.txt
similarity index 100%
rename from python/prototype/requirements.txt
rename to proto/prototype/requirements.txt
diff --git a/python/prototype/run_cli.py b/proto/prototype/run_cli.py
similarity index 100%
rename from python/prototype/run_cli.py
rename to proto/prototype/run_cli.py
diff --git a/python/prototype/run_gui.py b/proto/prototype/run_gui.py
similarity index 100%
rename from python/prototype/run_gui.py
rename to proto/prototype/run_gui.py
diff --git a/python/prototype/src/fastestcopy/__init__.py b/proto/prototype/src/fastestcopy/__init__.py
similarity index 100%
rename from python/prototype/src/fastestcopy/__init__.py
rename to proto/prototype/src/fastestcopy/__init__.py
diff --git a/python/prototype/src/fastestcopy/cli.py b/proto/prototype/src/fastestcopy/cli.py
similarity index 100%
rename from python/prototype/src/fastestcopy/cli.py
rename to proto/prototype/src/fastestcopy/cli.py
diff --git a/python/prototype/src/fastestcopy/engine/__init__.py b/proto/prototype/src/fastestcopy/engine/__init__.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/__init__.py
rename to proto/prototype/src/fastestcopy/engine/__init__.py
diff --git a/python/prototype/src/fastestcopy/engine/copier.py b/proto/prototype/src/fastestcopy/engine/copier.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/copier.py
rename to proto/prototype/src/fastestcopy/engine/copier.py
diff --git a/python/prototype/src/fastestcopy/engine/diskspace.py b/proto/prototype/src/fastestcopy/engine/diskspace.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/diskspace.py
rename to proto/prototype/src/fastestcopy/engine/diskspace.py
diff --git a/python/prototype/src/fastestcopy/engine/planner.py b/proto/prototype/src/fastestcopy/engine/planner.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/planner.py
rename to proto/prototype/src/fastestcopy/engine/planner.py
diff --git a/python/prototype/src/fastestcopy/engine/policy.py b/proto/prototype/src/fastestcopy/engine/policy.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/policy.py
rename to proto/prototype/src/fastestcopy/engine/policy.py
diff --git a/python/prototype/src/fastestcopy/engine/preview.py b/proto/prototype/src/fastestcopy/engine/preview.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/preview.py
rename to proto/prototype/src/fastestcopy/engine/preview.py
diff --git a/python/prototype/src/fastestcopy/engine/scanner.py b/proto/prototype/src/fastestcopy/engine/scanner.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/scanner.py
rename to proto/prototype/src/fastestcopy/engine/scanner.py
diff --git a/python/prototype/src/fastestcopy/engine/stats.py b/proto/prototype/src/fastestcopy/engine/stats.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/stats.py
rename to proto/prototype/src/fastestcopy/engine/stats.py
diff --git a/python/prototype/src/fastestcopy/engine/winio.py b/proto/prototype/src/fastestcopy/engine/winio.py
similarity index 100%
rename from python/prototype/src/fastestcopy/engine/winio.py
rename to proto/prototype/src/fastestcopy/engine/winio.py
diff --git a/python/prototype/src/fastestcopy/gui/__init__.py b/proto/prototype/src/fastestcopy/gui/__init__.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/__init__.py
rename to proto/prototype/src/fastestcopy/gui/__init__.py
diff --git a/python/prototype/src/fastestcopy/gui/app.py b/proto/prototype/src/fastestcopy/gui/app.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/app.py
rename to proto/prototype/src/fastestcopy/gui/app.py
diff --git a/python/prototype/src/fastestcopy/gui/copy_dialog.py b/proto/prototype/src/fastestcopy/gui/copy_dialog.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/copy_dialog.py
rename to proto/prototype/src/fastestcopy/gui/copy_dialog.py
diff --git a/python/prototype/src/fastestcopy/gui/copy_log.py b/proto/prototype/src/fastestcopy/gui/copy_log.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/copy_log.py
rename to proto/prototype/src/fastestcopy/gui/copy_log.py
diff --git a/python/prototype/src/fastestcopy/gui/drives.py b/proto/prototype/src/fastestcopy/gui/drives.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/drives.py
rename to proto/prototype/src/fastestcopy/gui/drives.py
diff --git a/python/prototype/src/fastestcopy/gui/elevate.py b/proto/prototype/src/fastestcopy/gui/elevate.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/elevate.py
rename to proto/prototype/src/fastestcopy/gui/elevate.py
diff --git a/python/prototype/src/fastestcopy/gui/file_pane.py b/proto/prototype/src/fastestcopy/gui/file_pane.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/file_pane.py
rename to proto/prototype/src/fastestcopy/gui/file_pane.py
diff --git a/python/prototype/src/fastestcopy/gui/help_content.py b/proto/prototype/src/fastestcopy/gui/help_content.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/help_content.py
rename to proto/prototype/src/fastestcopy/gui/help_content.py
diff --git a/python/prototype/src/fastestcopy/gui/help_dialog.py b/proto/prototype/src/fastestcopy/gui/help_dialog.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/help_dialog.py
rename to proto/prototype/src/fastestcopy/gui/help_dialog.py
diff --git a/python/prototype/src/fastestcopy/gui/i18n.py b/proto/prototype/src/fastestcopy/gui/i18n.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/i18n.py
rename to proto/prototype/src/fastestcopy/gui/i18n.py
diff --git a/python/prototype/src/fastestcopy/gui/main_window.py b/proto/prototype/src/fastestcopy/gui/main_window.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/main_window.py
rename to proto/prototype/src/fastestcopy/gui/main_window.py
diff --git a/python/prototype/src/fastestcopy/gui/netbrowse.py b/proto/prototype/src/fastestcopy/gui/netbrowse.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/netbrowse.py
rename to proto/prototype/src/fastestcopy/gui/netbrowse.py
diff --git a/python/prototype/src/fastestcopy/gui/settings_dialog.py b/proto/prototype/src/fastestcopy/gui/settings_dialog.py
similarity index 100%
rename from python/prototype/src/fastestcopy/gui/settings_dialog.py
rename to proto/prototype/src/fastestcopy/gui/settings_dialog.py
diff --git a/python/prototype/tests/test_elevate.py b/proto/prototype/tests/test_elevate.py
similarity index 100%
rename from python/prototype/tests/test_elevate.py
rename to proto/prototype/tests/test_elevate.py
diff --git a/python/prototype/tests/test_engine.py b/proto/prototype/tests/test_engine.py
similarity index 100%
rename from python/prototype/tests/test_engine.py
rename to proto/prototype/tests/test_engine.py
diff --git a/python/prototype/tests/test_file_pane.py b/proto/prototype/tests/test_file_pane.py
similarity index 100%
rename from python/prototype/tests/test_file_pane.py
rename to proto/prototype/tests/test_file_pane.py
diff --git a/python/prototype/tests/test_i18n.py b/proto/prototype/tests/test_i18n.py
similarity index 100%
rename from python/prototype/tests/test_i18n.py
rename to proto/prototype/tests/test_i18n.py
diff --git a/python/prototype/tests/test_main_window.py b/proto/prototype/tests/test_main_window.py
similarity index 100%
rename from python/prototype/tests/test_main_window.py
rename to proto/prototype/tests/test_main_window.py
diff --git a/python/tests/benchmark_native.py b/proto/tests/benchmark_native.py
similarity index 100%
rename from python/tests/benchmark_native.py
rename to proto/tests/benchmark_native.py
diff --git a/python/tests/native_smoke.py b/proto/tests/native_smoke.py
similarity index 98%
rename from python/tests/native_smoke.py
rename to proto/tests/native_smoke.py
index d69e18f..b91d6e6 100644
--- a/python/tests/native_smoke.py
+++ b/proto/tests/native_smoke.py
@@ -9,7 +9,7 @@
 
 
 ROOT = Path(__file__).resolve().parents[2]
-QFC = ROOT / "dist" / "binary" / "QuickFileCopy_cli.exe"
+QFC = ROOT / "dist" / "QuickFileCopy_cli.exe"
 
 
 def digest(path: Path) -> str:
diff --git a/scripts/build.bat b/scripts/build.bat
new file mode 100644
index 0000000..4ebb7e7
--- /dev/null
+++ b/scripts/build.bat
@@ -0,0 +1,6 @@
+@echo off
+setlocal
+cd /d "%~dp0\.."
+echo [Build] Building QuickFileCopy...
+python scripts\build.py %*
+
diff --git a/build_native.py b/scripts/build.py
similarity index 71%
rename from build_native.py
rename to scripts/build.py
index f3ebbb2..c72c86a 100644
--- a/build_native.py
+++ b/scripts/build.py
@@ -7,10 +7,21 @@
 import subprocess
 import sys
 
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parent
+SRC = REPO_ROOT / "src"
+APP_DIR = SRC / "app"
+CLI_DIR = SRC / "cli"
+ENGINE_DIR = SRC / "engine"
+INTERMEDIATE = REPO_ROOT / "build" / "intermediate"
+DIST = REPO_ROOT / "dist"
 
 ROOT = Path(__file__).resolve().parent
 NATIVE = ROOT / "core" / "native"
 DIST = ROOT / "dist" / "binary"
+if str(SCRIPT_DIR) not in sys.path:
+    sys.path.insert(0, str(SCRIPT_DIR))
+import bundle_html
 
 
 def find_tool(names: tuple[str, ...]) -> Path | None:
@@ -39,8 +50,10 @@ def find_tool(names: tuple[str, ...]) -> Path | None:
 
 
 def run(command: list[str], label: str) -> None:
+def run(command: list[str], label: str, cwd: Path | None = None) -> None:
     print(f"\n[{label}] {' '.join(command)}")
     completed = subprocess.run(command, cwd=ROOT, text=True)
+    completed = subprocess.run(command, cwd=cwd or REPO_ROOT, text=True)
     if completed.returncode:
         raise SystemExit(completed.returncode)
 
@@ -60,8 +73,15 @@ def build() -> None:
         raise SystemExit(f"WebView2Loader.dll was not found: {webview_loader}")
 
     run([sys.executable, str(ROOT / "bundle_html.py")], "bundle-html")
+    INTERMEDIATE.mkdir(parents=True, exist_ok=True)
     DIST.mkdir(parents=True, exist_ok=True)
     resource_object = DIST / "QuickFileCopy_res.o"
+
+    # 1. Bundle HTML into build/intermediate/QuickFileCopy.html
+    bundled_html = INTERMEDIATE / "QuickFileCopy.html"
+    bundle_html.bundle(bundled_html)
+
+    resource_object = INTERMEDIATE / "QuickFileCopy_res.o"
     common = [
         str(compiler),
         "-O3",
@@ -77,14 +97,20 @@ def build() -> None:
         "-static-libstdc++",
         "-Wl,--gc-sections",
         f"-I{NATIVE / 'include'}",
+        f"-I{SRC}",
+        f"-I{ENGINE_DIR}",
+        f"-I{APP_DIR}",
     ]
 
+    # 2. CLI Build
     run(
         common
         + [
             "-municode",
             str(NATIVE / "src" / "copy_engine.cpp"),
             str(NATIVE / "src" / "main_cli.cpp"),
+            str(ENGINE_DIR / "copy_engine.cpp"),
+            str(CLI_DIR / "main_cli.cpp"),
             "-o",
             str(DIST / "QuickFileCopy_cli.exe"),
             "-lkernel32",
@@ -93,10 +119,25 @@ def build() -> None:
         ],
         "cli",
     )
+
+    # 3. Resource compilation (include APP_DIR and INTERMEDIATE for QuickFileCopy.html and .ico)
     run(
         [str(windres), str(NATIVE / "resources" / "QuickFileCopy.rc"), "-O", "coff", "-o", str(resource_object)],
+        [
+            str(windres),
+            f"-I{APP_DIR}",
+            f"-I{INTERMEDIATE}",
+            str(APP_DIR / "QuickFileCopy.rc"),
+            "-O",
+            "coff",
+            "-o",
+            str(resource_object),
+        ],
         "resource",
+        cwd=APP_DIR,
     )
+
+    # 4. GUI Build
     run(
         common
         + [
@@ -104,6 +145,8 @@ def build() -> None:
             f"-I{webview_include}",
             str(NATIVE / "src" / "copy_engine.cpp"),
             str(NATIVE / "src" / "webview_main.cpp"),
+            str(ENGINE_DIR / "copy_engine.cpp"),
+            str(APP_DIR / "main_gui.cpp"),
             str(resource_object),
             "-o",
             str(DIST / "QuickFileCopy.exe"),
@@ -118,11 +161,14 @@ def build() -> None:
         ],
         "gui",
     )
+
+    # 5. Copy WebView2Loader.dll
     shutil.copy2(webview_loader, DIST / "WebView2Loader.dll")
 
     resource_object.unlink(missing_ok=True)
     for path in (DIST / "QuickFileCopy.exe", DIST / "QuickFileCopy_cli.exe", DIST / "WebView2Loader.dll"):
         print(f"[ok] {path.relative_to(ROOT)} ({path.stat().st_size:,} bytes)")
+        print(f"[ok] {path.relative_to(REPO_ROOT)} ({path.stat().st_size:,} bytes)")
 
 
 if __name__ == "__main__":
diff --git a/bundle_html.py b/scripts/bundle_html.py
similarity index 52%
rename from bundle_html.py
rename to scripts/bundle_html.py
index 9c4f6d0..d4b7041 100644
--- a/bundle_html.py
+++ b/scripts/bundle_html.py
@@ -7,14 +7,28 @@
 ROOT = Path(__file__).resolve().parent
 SOURCE = ROOT / "templates" / "index.html"
 OUTPUT = ROOT / "core" / "native" / "resources" / "QuickFileCopy.html"
+SCRIPT_DIR = Path(__file__).resolve().parent
+REPO_ROOT = SCRIPT_DIR.parent
+SOURCE = REPO_ROOT / "src" / "ui" / "index.html"
+OUTPUT = REPO_ROOT / "build" / "intermediate" / "QuickFileCopy.html"
 
 
 def main() -> None:
+def bundle(output_path: Path | None = None) -> Path:
+    target = output_path or OUTPUT
     if not SOURCE.exists():
         raise SystemExit(f"UI template was not found: {SOURCE}")
     OUTPUT.parent.mkdir(parents=True, exist_ok=True)
     shutil.copyfile(SOURCE, OUTPUT)
     print(f"[ok] bundled UI: {OUTPUT.relative_to(ROOT)}")
+    target.parent.mkdir(parents=True, exist_ok=True)
+    shutil.copyfile(SOURCE, target)
+    print(f"[ok] bundled UI: {target.relative_to(REPO_ROOT)}")
+    return target
+
+
+def main() -> None:
+    bundle()
 
 
 if __name__ == "__main__":
diff --git a/core/native/resources/QuickFileCopy.ico b/src/app/QuickFileCopy.ico
similarity index 100%
rename from core/native/resources/QuickFileCopy.ico
rename to src/app/QuickFileCopy.ico
diff --git a/core/native/resources/QuickFileCopy.rc b/src/app/QuickFileCopy.rc
similarity index 91%
rename from core/native/resources/QuickFileCopy.rc
rename to src/app/QuickFileCopy.rc
index e6df9b0..6985695 100644
--- a/core/native/resources/QuickFileCopy.rc
+++ b/src/app/QuickFileCopy.rc
@@ -2,6 +2,8 @@
 
 IDI_APP_ICON ICON "core/native/resources/QuickFileCopy.ico"
 IDR_APP_HTML RCDATA "core/native/resources/QuickFileCopy.html"
+IDI_APP_ICON ICON "QuickFileCopy.ico"
+IDR_APP_HTML RCDATA "QuickFileCopy.html"
 
 1 VERSIONINFO
  FILEVERSION 1,0,0,0
diff --git a/core/native/src/webview_main.cpp b/src/app/main_gui.cpp
similarity index 99%
rename from core/native/src/webview_main.cpp
rename to src/app/main_gui.cpp
index 374c445..3110738 100644
--- a/core/native/src/webview_main.cpp
+++ b/src/app/main_gui.cpp
@@ -9,6 +9,7 @@
 
 #include "qfc/copy_engine.h"
 #include "../resources/resource.h"
+#include "resource.h"
 
 #include <algorithm>
 #include <atomic>
diff --git a/core/native/resources/resource.h b/src/app/resource.h
similarity index 100%
rename from core/native/resources/resource.h
rename to src/app/resource.h
diff --git a/core/native/src/main_cli.cpp b/src/cli/main_cli.cpp
similarity index 100%
rename from core/native/src/main_cli.cpp
rename to src/cli/main_cli.cpp
diff --git a/core/native/src/copy_engine.cpp b/src/engine/copy_engine.cpp
similarity index 100%
rename from core/native/src/copy_engine.cpp
rename to src/engine/copy_engine.cpp
diff --git a/core/native/include/qfc/copy_engine.h b/src/engine/qfc/copy_engine.h
similarity index 100%
rename from core/native/include/qfc/copy_engine.h
rename to src/engine/qfc/copy_engine.h
diff --git a/static/css/.gitkeep b/src/ui/css/.gitkeep
similarity index 100%
rename from static/css/.gitkeep
rename to src/ui/css/.gitkeep
diff --git a/static/img/.gitkeep b/src/ui/img/.gitkeep
similarity index 100%
rename from static/img/.gitkeep
rename to src/ui/img/.gitkeep
diff --git a/templates/index.html b/src/ui/index.html
similarity index 100%
rename from templates/index.html
rename to src/ui/index.html
diff --git a/static/js/.gitkeep b/src/ui/js/.gitkeep
similarity index 100%
rename from static/js/.gitkeep
rename to src/ui/js/.gitkeep
diff --git a/static/README.md b/static/README.md
deleted file mode 100644
index b0b8fc8..0000000
--- a/static/README.md
+++ /dev/null
@@ -1,5 +0,0 @@
-# Static UI assets
-
-QuickFileCopy keeps its CSS and JavaScript inline in `templates/index.html` so the
-WebView2 UI can be embedded as one resource. This directory is reserved for a future split
-into `css/`, `js/`, and `img/`; `bundle_html.py` is the single bundling entry point.