.gitignore

@@ -9,8 +9,3 @@ debug
 hid-nintendo.c
 __pycache__
 !.vscode/*
-.omo/*
-.slim/*
-pytest-*/*
-build-*/*
-.ignore

ADAPTER_PARITY_PLAN.md

@@ -427,7 +427,7 @@ with the current identity.
 
 #### 4A — Output-driver boundary and production XInput
 
-- replace `SWITCH_PICO_ADAPTER_FEASIBILITY` branches in `src/firmware/main.cpp` with
+- replace `SWITCH_PICO_ADAPTER_FEASIBILITY` branches in `switch-pico.cpp` with
   one fixed static driver interface: descriptors, init/reset, input, task,
   readiness/capabilities, and host output
 - keep the Phase 3 profile/runtime transform exactly once before serialization

CMakeLists.txt

@@ -56,29 +56,26 @@ pico_sdk_init()
 
 # Configure BLUEPAD32 input backend if selected
 if(SWITCH_PICO_INPUT_BACKEND STREQUAL "BLUEPAD32")
+    # Ensure Python3 is available and execute patch preparation
     find_package(Python3 REQUIRED COMPONENTS Interpreter)
-
+    
     set(BLUEPAD32_PREP_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/tools/prepare_bluepad32.py)
-    set(BLUEPAD32_SOURCE ${CMAKE_CURRENT_LIST_DIR}/external/bluepad32)
-    set(BLUEPAD32_PATCH ${CMAKE_CURRENT_LIST_DIR}/patches/bluepad32-sdl3-imu.patch)
-    set(BLUEPAD32_ROOT ${CMAKE_CURRENT_BINARY_DIR}/_deps/bluepad32-src)
     execute_process(
         COMMAND ${Python3_EXECUTABLE} ${BLUEPAD32_PREP_SCRIPT}
-                --bluepad32 ${BLUEPAD32_SOURCE}
-                --patch ${BLUEPAD32_PATCH}
-                --output ${BLUEPAD32_ROOT}
         WORKING_DIRECTORY ${CMAKE_CURRENT_LIST_DIR}
         RESULT_VARIABLE BLUEPAD32_PREP_RESULT
         OUTPUT_VARIABLE BLUEPAD32_PREP_OUTPUT
         ERROR_VARIABLE BLUEPAD32_PREP_ERROR
     )
-
+    
     if(NOT BLUEPAD32_PREP_RESULT EQUAL 0)
         message(FATAL_ERROR
-            "Failed to prepare isolated Bluepad32 source. "
+            "Failed to prepare Bluepad32: Patch application or validation failed. "
             "Details: ${BLUEPAD32_PREP_ERROR}")
     endif()
-
+    
+    # Configure Bluepad32 include paths and subdirectory
+    set(BLUEPAD32_ROOT ${CMAKE_CURRENT_LIST_DIR}/external/bluepad32)
     set(BTSTACK_ROOT ${PICO_SDK_PATH}/lib/btstack)
     include_directories(
             ${CMAKE_CURRENT_LIST_DIR}/bluepad32_config
@@ -92,37 +89,36 @@ if(SWITCH_PICO_INPUT_BACKEND STREQUAL "BLUEPAD32")
     )
 endif()
 
-# Firmware sources live under one include root and are grouped by responsibility.
-set(SWITCH_PICO_SOURCE_DIR ${CMAKE_CURRENT_LIST_DIR}/src/firmware)
+# Add executable. Default name is the project name, version 0.1
 
 add_executable(switch-pico
-        ${SWITCH_PICO_SOURCE_DIR}/main.cpp
-        ${SWITCH_PICO_SOURCE_DIR}/usb/usb_output_driver.cpp
-        ${SWITCH_PICO_SOURCE_DIR}/usb/switch/switch_pro_driver.cpp
-        ${SWITCH_PICO_SOURCE_DIR}/usb/switch/switch_haptics.cpp
+        switch-pico.cpp
+        switch_pro_driver.cpp
+        usb_output_driver.cpp
+        switch_haptics.cpp
 )
 if(SWITCH_PICO_INPUT_BACKEND STREQUAL "BLUEPAD32")
     target_sources(switch-pico PRIVATE
-            ${SWITCH_PICO_SOURCE_DIR}/adapter/adapter_host_probe.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/adapter/adapter_mode_controller.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/configuration/adapter_configuration.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/configuration/configuration_service.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/configuration/configuration_storage.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/configuration/configuration_transaction.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/core/controller_identity.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/input/bluepad32_input_backend.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/platform/pico/bootsel_pairing_button.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/platform/pico/pico_configuration_storage.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/platform/pico/pico_profile_storage.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/controller_profile.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/controller_profile_runtime.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/controller_profile_transform.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/controller_synthetic_input.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/profile_service.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/profile/profile_storage.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/usb/generic_hid/generic_hid_driver.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/usb/usb_configuration_management.cpp
-            ${SWITCH_PICO_SOURCE_DIR}/usb/xinput/xinput_driver.cpp
+            bluepad32_input_backend.cpp
+            adapter_host_probe.cpp
+            adapter_mode_controller.cpp
+            controller_identity.cpp
+            controller_profile.cpp
+            controller_profile_transform.cpp
+            controller_synthetic_input.cpp
+            controller_profile_runtime.cpp
+            profile_storage.cpp
+            profile_service.cpp
+            pico_profile_storage.cpp
+            bootsel_pairing_button.cpp
+            adapter_configuration.cpp
+            configuration_storage.cpp
+            configuration_transaction.cpp
+            configuration_service.cpp
+            pico_configuration_storage.cpp
+            usb_configuration_management.cpp
+            xinput_driver.cpp
+            generic_hid_driver.cpp
     )
     target_compile_definitions(switch-pico PRIVATE
             SWITCH_PICO_BLUEPAD32=1
@@ -170,11 +166,9 @@ if (SWITCH_PICO_LOG)
     target_compile_definitions(switch-pico PRIVATE SWITCH_PICO_LOG=1)
 endif()
 
-# Internal includes are rooted at src/firmware. TinyUSB discovers tusb_config.h
-# through the Pico platform directory.
+# Add the standard include files to the build
 target_include_directories(switch-pico PRIVATE
-        ${SWITCH_PICO_SOURCE_DIR}
-        ${SWITCH_PICO_SOURCE_DIR}/platform/pico
+        ${CMAKE_CURRENT_LIST_DIR}
 )
 
 pico_add_extra_outputs(switch-pico)

README.md

@@ -3,31 +3,11 @@
 Raspberry Pi Pico firmware that emulates one or more Switch Pro controllers over USB. Input can come from the SDL3-to-UART computer bridge or, on Pico 2 W, directly from Bluetooth controllers through Bluepad32.
 
 ## What you get
-- **Firmware** (`src/firmware/`): acts as a Switch Pro controller (one on standard Pico, four on Pico 2 W AIO), accepting either UART bridge reports or the optional Pico 2 W Bluepad32 backend.
+- **Firmware** (`switch-pico.cpp` + `switch_pro_driver.*`): acts as a Switch Pro controller (one on standard Pico, four on Pico 2 W AIO), accepting either UART bridge reports or the optional Pico 2 W Bluepad32 backend.
 - **Python bridge** (`switch_pico_bridge.controller_uart_bridge` / CLI `controller-uart-bridge`): reads SDL3 controllers on the host, sends reports over UART, and applies rumble locally. Hot‑plug friendly and cross‑platform (macOS/Windows/Linux).
-- **Color configuration** (`src/firmware/platform/pico/controller_color_config.h`): compile-time RGB colors for emulated controller grips and supported Bluetooth controller LEDs.
+- **Color configuration** (`controller_color_config.h`): compile-time RGB colors for emulated controller grips and supported Bluetooth controller LEDs.
 - **Pico 2 W AIO firmware** (`firmware/switch-pico-aio.uf2`): hosts four concurrent Bluetooth controllers and sends their controls, calibrated motion, rumble, and slot identity through four separate Switch Pro USB interfaces without a computer.
 
-## Source layout
-
-Firmware code has one include root, `src/firmware`, with responsibility-based
-modules:
-
-| Path | Responsibility |
-|---|---|
-| `src/firmware/main.cpp` | Firmware entry point and backend orchestration |
-| `src/firmware/adapter/` | USB mode selection, host probing, and managed reboot |
-| `src/firmware/configuration/` | Persistent adapter configuration and transactions |
-| `src/firmware/core/` | Shared controller identity, color, and input-state types |
-| `src/firmware/input/` | Bluepad32 controller input backend and hotkeys |
-| `src/firmware/platform/pico/` | Pico flash/BOOTSEL integrations and compile-time board configuration |
-| `src/firmware/profile/` | Controller profiles, transforms, storage, and runtime |
-| `src/firmware/usb/` | USB output boundary, management protocol, and per-protocol drivers |
-
-Internal includes are rooted at `src/firmware`, for example
-`#include "profile/controller_profile.h"`. Host-side Python remains in
-`src/switch_pico_bridge/`; native firmware tests remain in `tests/`.
-
 ## Quick start
 1. Flash the Pico with `firmware/switch-pico.uf2` (or build your own) using BOOTSEL drag-and-drop (see “Manual UF2 flashing” below).
 2. Wire Pico UART1 to a USB↔UART adapter (GPIO4 TX, GPIO5 RX, GND) and plug that adapter into your host PC.
@@ -64,7 +44,7 @@ This uses an isolated `build-aio/` CMake cache and publishes:
 
 The default `python3 build.py` command and `firmware/switch-pico.*` artifacts remain the UART/Pico build. The AIO build requires `PICO_BOARD=pico2_w`; it is not interchangeable with the original non-wireless Pico firmware.
 
-Both `build.py --aio` and direct AIO CMake configuration copy the pinned Bluepad32 source into the active build directory and apply `patches/bluepad32-sdl3-imu.patch` there before compiling. The patch makes supported motion controllers use SDL3-equivalent axes and fixed-point units before conversion to Nintendo samples. The `external/bluepad32` submodule remains pristine; patch or source-revision drift fails configuration.
+Both `build.py --aio` and direct AIO CMake configuration apply `patches/bluepad32-sdl3-imu.patch` idempotently before compiling Bluepad32. The patch makes supported motion controllers use SDL3-equivalent axes and fixed-point units before conversion to Nintendo samples. It intentionally leaves the dependency worktree dirty; the committed submodule revision remains Bluepad32 4.2.0.
 
 ### Pairing up to four controllers
 
@@ -182,7 +162,7 @@ Each AIO slot has one color shared by its emulated Switch Pro grips and its phys
 3. Yellow `#F6C945`
 4. Green `#2ECC71`
 
-When a controller becomes ready, RGB-capable devices such as DualSense and DualShock 4 receive a darker, more saturated RGB value derived automatically from the slot's Switch grip color. Controllers without an RGB light use player indicator 1, 2, 3, or 4 when Bluepad32 exposes player-LED control. Devices without either capability are left unchanged. Edit only the four grip colors in `src/firmware/platform/pico/controller_color_config.h`; rebuilding automatically recalibrates their lightbar colors.
+When a controller becomes ready, RGB-capable devices such as DualSense and DualShock 4 receive a darker, more saturated RGB value derived automatically from the slot's Switch grip color. Controllers without an RGB light use player indicator 1, 2, 3, or 4 when Bluepad32 exposes player-LED control. Devices without either capability are left unchanged. Edit only the four grip colors in `controller_color_config.h`; rebuilding automatically recalibrates their lightbar colors.
 
 ### Controller capabilities
 
@@ -372,7 +352,7 @@ python3 build.py --grip-color FF00AA
 ```
 
 Both options update all four slot definitions in
-`src/firmware/platform/pico/controller_color_config.h` before building. With no color option, the
+`controller_color_config.h` before building. With no color option, the
 per-slot blue/red/yellow/green palette is left unchanged. Run
 `python3 build.py --help` to see the available command-line options.
 
@@ -567,7 +547,7 @@ Keep `SwitchImuMode` as a three-state value. Never acknowledge mode 2 and then e
 
 #### Mode-2 implementation
 
-`src/firmware/usb/switch/switch_pro_driver.cpp` implements this in `integrate_motion_sample()` and `fill_quaternion_imu_report_data()`:
+`switch_pro_driver.cpp` implements this in `integrate_motion_sample()` and `fill_quaternion_imu_report_data()`:
 
 1. Reset quaternion state to `(0, 0, 0, 1)` when transitioning into mode 2.
 2. Integrate each report's three gyro samples at 5 ms per sample. The Nintendo quaternion axes use sensor `Y, X, Z`, not `X, Y, Z`.

adapter_configuration.cpp

@@ -1,4 +1,4 @@
-#include "configuration/adapter_configuration.h"
+#include "adapter_configuration.h"
 
 namespace {
 

adapter_configuration.h

@@ -3,7 +3,7 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "adapter/adapter_usb_mode.h"
+#include "adapter_usb_mode.h"
 
 constexpr uint16_t ADAPTER_CONFIGURATION_LEGACY_SCHEMA_VERSION = 1;
 constexpr uint16_t ADAPTER_CONFIGURATION_SCHEMA_VERSION = 2;

adapter_host_probe.cpp

@@ -1,4 +1,5 @@
-#include "adapter/adapter_host_probe.h"
+#include "adapter_host_probe.h"
+
 #include <stddef.h>
 #ifdef SWITCH_PICO_LOG
 #include <stdio.h>
@@ -7,12 +8,12 @@
 #define PROBE_LOG(...) ((void)0)
 #endif
 
-#include "adapter/adapter_host_probe_state.h"
-#include "profile/controller_profile_runtime.h"
+#include "adapter_host_probe_state.h"
+#include "controller_profile_runtime.h"
 #include "hardware/structs/watchdog.h"
 #include "hardware/watchdog.h"
 #include "pico/time.h"
-#include "usb/xinput/xinput_descriptors.h"
+#include "xinput_descriptors.h"
 
 namespace {
 

adapter_host_probe.h

@@ -2,7 +2,7 @@
 
 #include <stdint.h>
 
-#include "adapter/adapter_usb_mode.h"
+#include "adapter_usb_mode.h"
 #include "tusb.h"
 
 // Consume watchdog scratch and freeze the active mode. Call exactly once

adapter_mode_controller.cpp

@@ -1,15 +1,16 @@
-#include "adapter/adapter_mode_controller.h"
-#include "adapter/adapter_reboot.h"
-#include "configuration/adapter_configuration.h"
-#include "adapter/adapter_host_probe.h"
-#include "input/bluepad32_input_backend.h"
-#include "configuration/configuration_service.h"
-#include "profile/controller_profile.h"
-#include "profile/controller_profile_runtime.h"
+#include "adapter_mode_controller.h"
+#include "adapter_reboot.h"
+
+#include "adapter_configuration.h"
+#include "adapter_host_probe.h"
+#include "bluepad32_input_backend.h"
+#include "configuration_service.h"
+#include "controller_profile.h"
+#include "controller_profile_runtime.h"
 #include "hardware/watchdog.h"
 #include "pico/bootrom.h"
 #include "tusb.h"
-#include "usb/usb_output_driver.h"
+#include "usb_output_driver.h"
 
 namespace {
 

adapter_mode_controller.h

@@ -2,8 +2,8 @@
 
 #include <stdint.h>
 
-#include "adapter/adapter_usb_mode.h"
-#include "core/controller_state.h"
+#include "adapter_usb_mode.h"
+#include "controller_state.h"
 
 constexpr uint8_t ADAPTER_MODE_CONTROLLER_SLOT_COUNT = 4;
 constexpr uint32_t ADAPTER_MODE_CHORD_HOLD_MS = 3000;

bluepad32_input_backend.cpp

@@ -1,7 +1,8 @@
-#include "input/bluepad32_input_backend.h"
-#include "input/controller_hotkey_config.h"
-#include "configuration/configuration_service.h"
-#include "profile/profile_service.h"
+#include "bluepad32_input_backend.h"
+#include "controller_hotkey_config.h"
+#include "configuration_service.h"
+#include "profile_service.h"
+
 #include <limits.h>
 #include <stddef.h>
 #include <string.h>
@@ -14,7 +15,7 @@
 #include <pico/stdlib.h>
 #include <uni.h>
 #ifdef SWITCH_PICO_USB_OUTPUT_MODES
-#include "adapter/adapter_usb_mode.h"
+#include "adapter_usb_mode.h"
 #endif
 
 namespace {

bluepad32_input_backend.h

@@ -2,11 +2,11 @@
 
 #include <stdint.h>
 
-#include "core/controller_color.h"
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "core/controller_state.h"
-#include "usb/switch/switch_haptics.h"
+#include "controller_color.h"
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "controller_state.h"
+#include "switch_haptics.h"
 
 constexpr uint8_t BLUEPAD32_INPUT_BACKEND_SLOT_COUNT = 4;
 constexpr uint8_t BLUEPAD32_PAIRING_RECORD_CAPACITY = 16;

bootsel_pairing_button.cpp

@@ -1,4 +1,5 @@
-#include "platform/pico/bootsel_pairing_button.h"
+#include "bootsel_pairing_button.h"
+
 #include "hardware/gpio.h"
 #include "hardware/structs/ioqspi.h"
 #include "hardware/structs/sio.h"

build.py

@@ -10,8 +10,7 @@ import sys
 from pathlib import Path
 
 SCRIPT_DIR = Path(__file__).resolve().parent
-FIRMWARE_SOURCE_DIR = SCRIPT_DIR / "src" / "firmware"
-CONFIG_FILE = FIRMWARE_SOURCE_DIR / "platform" / "pico" / "controller_color_config.h"
+CONFIG_FILE = SCRIPT_DIR / "controller_color_config.h"
 BUILD_DIR = SCRIPT_DIR / "build"
 AIO_BUILD_DIR = SCRIPT_DIR / "build-aio"
 FEASIBILITY_BUILD_DIR = SCRIPT_DIR / "build-feasibility"
@@ -266,7 +265,7 @@ def parse_args():
     parser = argparse.ArgumentParser(
         description="Build and flash the project, optionally setting grip colors.",
         formatter_class=argparse.RawDescriptionHelpFormatter,
-        epilog=f"Default behavior leaves {CONFIG_FILE.relative_to(SCRIPT_DIR)} unchanged.",
+        epilog="Default behavior leaves controller_color_config.h unchanged.",
     )
     mode_group = parser.add_mutually_exclusive_group()
     mode_group.add_argument(
@@ -366,6 +365,7 @@ def build(
     firmware_uf2_path,
 ):
     if aio or adapter_feasibility:
+        run_cmd([sys.executable, str(SCRIPT_DIR / "tools" / "prepare_bluepad32.py")])
         definitions = [
             "-DSWITCH_PICO_LOG=OFF",
             "-DPICO_BOARD=pico2_w",

configuration_service.cpp

@@ -1,8 +1,9 @@
-#include "configuration/configuration_service.h"
+#include "configuration_service.h"
+
 #include <string.h>
 
 #include "pico/critical_section.h"
-#include "platform/pico/pico_configuration_storage.h"
+#include "pico_configuration_storage.h"
 
 namespace {
 

configuration_service.h

@@ -3,8 +3,8 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "configuration/adapter_configuration.h"
-#include "configuration/configuration_transaction.h"
+#include "adapter_configuration.h"
+#include "configuration_transaction.h"
 
 constexpr uint32_t CONFIGURATION_SERVICE_INTERNAL_TRANSACTION_ID_MASK =
     0x80000000u;

configuration_storage.cpp

@@ -1,4 +1,5 @@
-#include "configuration/configuration_storage.h"
+#include "configuration_storage.h"
+
 #include <string.h>
 
 namespace {

configuration_transaction.cpp

@@ -1,7 +1,9 @@
-#include "configuration/configuration_transaction.h"
+#include "configuration_transaction.h"
+
 #include <string.h>
 
-#include "configuration/adapter_configuration.h"
+#include "adapter_configuration.h"
+
 ConfigurationTransactionStatus ConfigurationTransaction::begin(
     uint32_t transaction_id, uint16_t schema_version, size_t payload_size,
     uint32_t payload_crc) {

configuration_transaction.h

@@ -3,7 +3,7 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "configuration/configuration_storage.h"
+#include "configuration_storage.h"
 
 enum class ConfigurationTransactionStatus : uint8_t {
     kIdle = 0,

controller_identity.cpp

@@ -1,4 +1,5 @@
-#include "core/controller_identity.h"
+#include "controller_identity.h"
+
 #include <string.h>
 
 namespace {

controller_profile.cpp

@@ -1,4 +1,5 @@
-#include "profile/controller_profile.h"
+#include "controller_profile.h"
+
 #include <string.h>
 
 namespace {

controller_profile.h

@@ -3,7 +3,7 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "core/controller_identity.h"
+#include "controller_identity.h"
 
 constexpr uint16_t CONTROLLER_PROFILE_LEGACY_SCHEMA_VERSION = 1;
 constexpr uint16_t CONTROLLER_PROFILE_SCHEMA_VERSION = 2;

controller_profile_runtime.cpp

@@ -1,8 +1,9 @@
-#include "profile/controller_profile_runtime.h"
-#include "configuration/configuration_service.h"
-#include "core/controller_identity.h"
-#include "profile/controller_synthetic_input.h"
-#include "profile/profile_service.h"
+#include "controller_profile_runtime.h"
+
+#include "configuration_service.h"
+#include "controller_identity.h"
+#include "controller_synthetic_input.h"
+#include "profile_service.h"
 
 namespace {
 

controller_profile_runtime.h

@@ -2,10 +2,10 @@
 
 #include <stdint.h>
 
-#include "adapter/adapter_usb_mode.h"
+#include "adapter_usb_mode.h"
 
-#include "input/bluepad32_input_backend.h"
-#include "profile/controller_profile_transform.h"
+#include "bluepad32_input_backend.h"
+#include "controller_profile_transform.h"
 
 constexpr uint8_t CONTROLLER_PROFILE_RUNTIME_SLOT_COUNT = 4;
 constexpr uint16_t CONTROLLER_PROFILE_DEFAULT_SWITCHING_CHORD =

controller_profile_transform.cpp

@@ -1,4 +1,5 @@
-#include "profile/controller_profile_transform.h"
+#include "controller_profile_transform.h"
+
 #include <limits.h>
 
 namespace {

controller_profile_transform.h

@@ -2,9 +2,9 @@
 
 #include <stdint.h>
 
-#include "profile/controller_profile.h"
-#include "core/controller_state.h"
-#include "usb/switch/switch_haptics.h"
+#include "controller_profile.h"
+#include "controller_state.h"
+#include "switch_haptics.h"
 
 struct ControllerProfileTransformResult {
     ControllerState state{};

controller_synthetic_input.cpp

@@ -1,4 +1,4 @@
-#include "profile/controller_synthetic_input.h"
+#include "controller_synthetic_input.h"
 
 namespace {
 

controller_synthetic_input.h

@@ -2,7 +2,7 @@
 
 #include <stdint.h>
 
-#include "profile/controller_profile_transform.h"
+#include "controller_profile_transform.h"
 
 struct ControllerSyntheticBindingState {
     bool active = false;

generic_hid_descriptors.h

@@ -3,7 +3,7 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "core/controller_state.h"
+#include "controller_state.h"
 
 #ifndef SWITCH_PICO_HID_INSTANCE_COUNT
 #define SWITCH_PICO_HID_INSTANCE_COUNT 1

generic_hid_driver.cpp

@@ -1,7 +1,8 @@
-#include "usb/generic_hid/generic_hid_driver.h"
+#include "generic_hid_driver.h"
+
 #include <string.h>
 
-#include "usb/generic_hid/generic_hid_descriptors.h"
+#include "generic_hid_descriptors.h"
 
 namespace {
 

generic_hid_driver.h

@@ -2,9 +2,8 @@
 
 #include <stdint.h>
 
-#include "core/controller_state.h"
+#include "controller_state.h"
 #include "tusb.h"
-
 namespace GenericHid {
 
 enum class ReportDescriptorVariant : uint8_t {

pico_configuration_storage.cpp

@@ -1,4 +1,5 @@
-#include "platform/pico/pico_configuration_storage.h"
+#include "pico_configuration_storage.h"
+
 #include <string.h>
 
 #include "hardware/flash.h"

pico_configuration_storage.h

@@ -1,5 +1,5 @@
 #pragma once
 
-#include "configuration/configuration_storage.h"
+#include "configuration_storage.h"
 
 ConfigurationStorageIo pico_configuration_storage_io();

pico_profile_storage.cpp

@@ -1,7 +1,8 @@
-#include "platform/pico/pico_profile_storage.h"
+#include "pico_profile_storage.h"
+
 #include <string.h>
 
-#include "configuration/configuration_storage.h"
+#include "configuration_storage.h"
 #include "hardware/flash.h"
 #include "pico/btstack_flash_bank.h"
 #include "pico/flash.h"

pico_profile_storage.h

@@ -1,5 +1,5 @@
 #pragma once
 
-#include "profile/profile_storage.h"
+#include "profile_storage.h"
 
 ProfileStorageIo pico_profile_storage_io();

profile_service.cpp

@@ -1,9 +1,10 @@
-#include "profile/profile_service.h"
+#include "profile_service.h"
+
 #include <string.h>
 
 #include "pico/critical_section.h"
-#include "platform/pico/pico_profile_storage.h"
-#include "profile/profile_storage.h"
+#include "pico_profile_storage.h"
+#include "profile_storage.h"
 
 namespace {
 

profile_service.h

@@ -3,8 +3,8 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "configuration/configuration_transaction.h"
-#include "profile/controller_profile.h"
+#include "configuration_transaction.h"
+#include "controller_profile.h"
 
 constexpr uint8_t PROFILE_SERVICE_LIST_CAPACITY =
     CONTROLLER_PROFILE_STABLE_IDENTITY_CAPACITY + 1;

profile_storage.cpp

@@ -1,4 +1,5 @@
-#include "profile/profile_storage.h"
+#include "profile_storage.h"
+
 #include <string.h>
 
 namespace {

profile_storage.h

@@ -3,7 +3,7 @@
 #include <stddef.h>
 #include <stdint.h>
 
-#include "profile/controller_profile.h"
+#include "controller_profile.h"
 
 constexpr uint8_t PROFILE_STORAGE_BANK_COUNT = 2;
 constexpr size_t PROFILE_STORAGE_SECTOR_SIZE = 4096;

switch-pico.cpp

@@ -2,15 +2,15 @@
 #include "bsp/board.h"
 #include "pico/stdlib.h"
 #include "tusb.h"
-#include "usb/switch/switch_pro_driver.h"
-#include "usb/usb_output_driver.h"
+#include "switch_pro_driver.h"
+#include "usb_output_driver.h"
 #ifndef SWITCH_PICO_BLUEPAD32
 #include "hardware/uart.h"
 #else
-#include "adapter/adapter_mode_controller.h"
-#include "input/bluepad32_input_backend.h"
-#include "platform/pico/bootsel_pairing_button.h"
-#include "profile/controller_profile_runtime.h"
+#include "adapter_mode_controller.h"
+#include "bluepad32_input_backend.h"
+#include "bootsel_pairing_button.h"
+#include "controller_profile_runtime.h"
 #endif
 
 #ifdef SWITCH_PICO_LOG

switch_haptics.cpp

@@ -1,4 +1,5 @@
-#include "usb/switch/switch_haptics.h"
+#include "switch_haptics.h"
+
 #include <cmath>
 #include <cstring>
 

switch_pro_driver.cpp

@@ -1,4 +1,4 @@
-#include "usb/switch/switch_pro_driver.h"
+#include "switch_pro_driver.h"
 
 #include <algorithm>
 #include <cstddef>
@@ -81,8 +81,8 @@ static SwitchProContext* context_for(uint8_t instance) {
 }
 
 // Optional compile-time color palette shared with Bluetooth controller LEDs.
-#if __has_include("platform/pico/controller_color_config.h")
-#include "platform/pico/controller_color_config.h"
+#if __has_include("controller_color_config.h")
+#include "controller_color_config.h"
 #endif
 #ifndef SWITCH_COLOR_BODY_R
 #define SWITCH_COLOR_BODY_R 0x1B

switch_pro_driver.h

@@ -8,11 +8,11 @@
 
 #include <stdbool.h>
 #include <stdint.h>
-#include "core/controller_color.h"
-#include "core/controller_state.h"
-#include "usb/switch/switch_haptics.h"
+#include "controller_color.h"
+#include "controller_state.h"
+#include "switch_haptics.h"
 #include "tusb.h"
-#include "usb/switch/switch_pro_descriptors.h"
+#include "switch_pro_descriptors.h"
 // Preserve the pre-neutral-state 35%-of-1023 digital trigger boundary.
 constexpr uint32_t SWITCH_PRO_LEGACY_TRIGGER_RANGE_MAXIMUM = 1023;
 constexpr uint32_t SWITCH_PRO_LEGACY_TRIGGER_PRESS_THRESHOLD = 358;

tests/adapter_host_probe_test.cpp

@@ -1,4 +1,5 @@
-#include "adapter/adapter_host_probe.h"
+#include "adapter_host_probe.h"
+
 #include <cstdint>
 #include <cstdlib>
 #include <cstring>
@@ -6,7 +7,7 @@
 
 #include "hardware/structs/watchdog.h"
 #include "pico/time.h"
-#include "usb/xinput/xinput_descriptors.h"
+#include "xinput_descriptors.h"
 
 namespace {
 

tests/adapter_mode_controller_test.cpp

@@ -1,15 +1,16 @@
-#include "adapter/adapter_mode_controller.h"
+#include "adapter_mode_controller.h"
+
 #include <algorithm>
 #include <cstdint>
 #include <cstdlib>
 #include <iostream>
 #include <vector>
 
-#include "configuration/adapter_configuration.h"
-#include "adapter/adapter_reboot.h"
-#include "input/bluepad32_input_backend.h"
-#include "configuration/configuration_service.h"
-#include "profile/controller_profile.h"
+#include "adapter_configuration.h"
+#include "adapter_reboot.h"
+#include "bluepad32_input_backend.h"
+#include "configuration_service.h"
+#include "controller_profile.h"
 
 namespace {
 

tests/bluepad32_backend_lifecycle_test.cpp

@@ -4,7 +4,7 @@
 #include <string>
 
 #include <uni.h>
-#include "platform/pico/controller_color_config.h"
+#include "../controller_color_config.h"
 
 namespace {
 
@@ -442,9 +442,8 @@ uint32_t btstack_run_loop_get_time_ms() {
 }
 
 
-#include "core/controller_identity.cpp"
-#include "input/bluepad32_input_backend.cpp"
-
+#include "../controller_identity.cpp"
+#include "../bluepad32_input_backend.cpp"
 namespace {
 void require_clear_completion_pending() {
     if (expected_pending_clear_token != 0) {

tests/bootsel_pairing_button_test.cpp

@@ -1,4 +1,5 @@
-#include "platform/pico/bootsel_pairing_button.h"
+#include "bootsel_pairing_button.h"
+
 #include <cstdlib>
 #include <cstdint>
 #include <iostream>

tests/configuration_service_test.cpp

@@ -1,7 +1,8 @@
-#include "configuration/adapter_configuration.h"
-#include "configuration/configuration_service.h"
-#include "configuration/configuration_storage.h"
-#include "platform/pico/pico_configuration_storage.h"
+#include "adapter_configuration.h"
+#include "configuration_service.h"
+#include "configuration_storage.h"
+#include "pico_configuration_storage.h"
+
 #include <cstdlib>
 #include <cstring>
 #include <iostream>

tests/configuration_storage_test.cpp

@@ -1,6 +1,7 @@
-#include "configuration/adapter_configuration.h"
-#include "configuration/configuration_storage.h"
-#include "configuration/configuration_transaction.h"
+#include "adapter_configuration.h"
+#include "configuration_storage.h"
+#include "configuration_transaction.h"
+
 #include <cstdlib>
 #include <cstring>
 #include <iostream>

tests/controller_profile_legacy_fixtures.h

@@ -2,7 +2,7 @@
 
 #include <stdint.h>
 
-#include "profile/controller_profile.h"
+#include "controller_profile.h"
 
 constexpr uint8_t kLegacyDefaultProfile[CONTROLLER_PROFILE_ENCODED_SIZE] = {
     0x01, 0x00, 0x00, 0x01, 0x00, 0x01, 0x02, 0x03, 0x04, 0x05, 0x06, 0x07, 0x08, 0x09, 0x0a, 0x0b,

tests/controller_profile_runtime_test.cpp

@@ -1,7 +1,9 @@
-#include "profile/controller_profile_runtime.h"
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "profile/profile_service.h"
+#include "controller_profile_runtime.h"
+
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "profile_service.h"
+
 #include <array>
 #include <cstdlib>
 #include <cstring>

tests/controller_profile_test.cpp

@@ -1,6 +1,6 @@
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "controller_profile_legacy_fixtures.h"
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "tests/controller_profile_legacy_fixtures.h"
 
 #include <cstdlib>
 #include <cstring>

tests/controller_profile_transform_test.cpp

@@ -1,6 +1,7 @@
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "profile/controller_profile_transform.h"
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "controller_profile_transform.h"
+
 #include <cstdlib>
 #include <cstring>
 #include <iostream>

tests/controller_synthetic_input_test.cpp

@@ -1,4 +1,5 @@
-#include "profile/controller_synthetic_input.h"
+#include "controller_synthetic_input.h"
+
 #include <array>
 #include <cstdlib>
 #include <cstring>

tests/generic_hid_descriptors_test.cpp

@@ -1,4 +1,5 @@
-#include "usb/generic_hid/generic_hid_descriptors.h"
+#include "generic_hid_descriptors.h"
+
 #include <array>
 #include <cstddef>
 #include <cstdint>

tests/generic_hid_driver_test.cpp

@@ -1,5 +1,7 @@
-#include "usb/generic_hid/generic_hid_driver.h"
-#include "usb/generic_hid/generic_hid_descriptors.h"
+#include "generic_hid_driver.h"
+
+#include "generic_hid_descriptors.h"
+
 #include <array>
 #include <cstddef>
 #include <cstdint>

tests/profile_service_test.cpp

@@ -1,8 +1,9 @@
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "platform/pico/pico_profile_storage.h"
-#include "profile/profile_service.h"
-#include "profile/profile_storage.h"
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "pico_profile_storage.h"
+#include "profile_service.h"
+#include "profile_storage.h"
+
 #include <cstdlib>
 #include <cstring>
 #include <iostream>

tests/profile_storage_test.cpp

@@ -1,7 +1,7 @@
-#include "core/controller_identity.h"
-#include "profile/controller_profile.h"
-#include "profile/profile_storage.h"
-#include "controller_profile_legacy_fixtures.h"
+#include "controller_identity.h"
+#include "controller_profile.h"
+#include "profile_storage.h"
+#include "tests/controller_profile_legacy_fixtures.h"
 
 #include <cstdlib>
 #include <cstring>

tests/switch_haptics_test.cpp

@@ -1,4 +1,5 @@
-#include "usb/switch/switch_haptics.h"
+#include "switch_haptics.h"
+
 #include <array>
 #include <cstdint>
 #include <iostream>

tests/switch_pro_descriptors_test.cpp

@@ -1,5 +1,6 @@
-#include "usb/switch/switch_pro_descriptors.h"
-#include "platform/pico/tusb_config.h"
+#include "switch_pro_descriptors.h"
+#include "tusb_config.h"
+
 #include <array>
 #include <cstddef>
 #include <cstdint>

tests/switch_pro_driver_context_test.cpp

@@ -1,6 +1,6 @@
-#include "usb/switch/switch_pro_driver.h"
-#include "usb/usb_output_driver.h"
-#include "platform/pico/controller_color_config.h"
+#include "switch_pro_driver.h"
+#include "usb_output_driver.h"
+#include "controller_color_config.h"
 #include "tusb.h"
 #include "pico/time.h"
 

tests/test_adapter_host_probe_native.py

@@ -20,8 +20,8 @@ def test_adapter_host_probe_native(tmp_path: Path) -> None:
             "-pedantic",
             "-DSWITCH_PICO_HID_INSTANCE_COUNT=4",
             f"-I{root / 'tests' / 'mode_native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
-            str(root / "src" / "firmware" / "adapter" / "adapter_host_probe.cpp"),
+            f"-I{root}",
+            str(root / "adapter_host_probe.cpp"),
             str(root / "tests" / "adapter_host_probe_test.cpp"),
             "-o",
             str(executable),

tests/test_adapter_mode_controller_native.py

@@ -20,8 +20,8 @@ def test_adapter_mode_controller_native(tmp_path: Path) -> None:
             "-pedantic",
             "-DSWITCH_PICO_HID_INSTANCE_COUNT=4",
             f"-I{root / 'tests' / 'mode_native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
-            str(root / "src" / "firmware" / "adapter" / "adapter_mode_controller.cpp"),
+            f"-I{root}",
+            str(root / "adapter_mode_controller.cpp"),
             str(root / "tests" / "adapter_mode_controller_test.cpp"),
             "-o",
             str(executable),

tests/test_bluepad32_backend_lifecycle_native.py

@@ -27,7 +27,7 @@ def test_bluepad32_backend_lifecycle_native(tmp_path: Path) -> None:
         command.extend(
             [
                 f"-I{root / 'tests' / 'bluepad32_native_stubs'}",
-                f"-I{root / 'src' / 'firmware'}",
+                f"-I{root}",
                 str(root / "tests" / "bluepad32_backend_lifecycle_test.cpp"),
                 "-o",
                 str(executable),

tests/test_bootsel_pairing_button_native.py

@@ -22,8 +22,8 @@ def test_bootsel_pairing_button_native(tmp_path: Path) -> None:
                 "-pedantic",
                 f"-DPICO_RP2350={rp2350}",
                 f"-I{root / 'tests' / 'bootsel_native_stubs'}",
-                f"-I{root / 'src' / 'firmware'}",
-                str(root / "src" / "firmware" / "platform" / "pico" / "bootsel_pairing_button.cpp"),
+                f"-I{root}",
+                str(root / "bootsel_pairing_button.cpp"),
                 str(root / "tests" / "bootsel_pairing_button_test.cpp"),
                 "-o",
                 str(executable),

tests/test_configuration_service_native.py

@@ -18,12 +18,12 @@ def test_configuration_service_native(tmp_path: Path) -> None:
             "-Werror",
             "-pedantic",
             f"-I{root / 'tests' / 'bluepad32_native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "configuration_service_test.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "adapter_configuration.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "configuration_service.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "configuration_storage.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "configuration_transaction.cpp"),
+            str(root / "adapter_configuration.cpp"),
+            str(root / "configuration_service.cpp"),
+            str(root / "configuration_storage.cpp"),
+            str(root / "configuration_transaction.cpp"),
             "-o",
             str(executable),
         ],

tests/test_configuration_storage_native.py

@@ -17,11 +17,11 @@ def test_configuration_storage_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "configuration_storage_test.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "adapter_configuration.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "configuration_storage.cpp"),
-            str(root / "src" / "firmware" / "configuration" / "configuration_transaction.cpp"),
+            str(root / "adapter_configuration.cpp"),
+            str(root / "configuration_storage.cpp"),
+            str(root / "configuration_transaction.cpp"),
             "-o",
             str(executable),
         ],

tests/test_controller_profile_native.py

@@ -17,10 +17,10 @@ def test_controller_profile_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "controller_profile_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
             "-o",
             str(executable),
         ],

tests/test_controller_profile_runtime_native.py

@@ -17,13 +17,13 @@ def test_controller_profile_runtime_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "controller_profile_runtime_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile_transform.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_synthetic_input.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile_runtime.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
+            str(root / "controller_profile_transform.cpp"),
+            str(root / "controller_synthetic_input.cpp"),
+            str(root / "controller_profile_runtime.cpp"),
             "-o",
             str(executable),
         ],

tests/test_controller_profile_transform_native.py

@@ -17,11 +17,11 @@ def test_controller_profile_transform_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "controller_profile_transform_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile_transform.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
+            str(root / "controller_profile_transform.cpp"),
             "-o",
             str(executable),
         ],

tests/test_controller_synthetic_input_native.py

@@ -17,12 +17,12 @@ def test_controller_synthetic_input_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "controller_synthetic_input_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile_transform.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_synthetic_input.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
+            str(root / "controller_profile_transform.cpp"),
+            str(root / "controller_synthetic_input.cpp"),
             "-o",
             str(executable),
         ],

tests/test_generic_hid_native.py

@@ -32,7 +32,7 @@ def compile_cpp(
         command.append(f"-I{root / 'tests' / 'native_stubs'}")
     command.extend(
         [
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             *[str(source) for source in sources],
             "-o",
             str(output),
@@ -98,7 +98,7 @@ def test_generic_hid_driver_contexts(tmp_path: Path) -> None:
         host_compiler(),
         executable,
         [
-            root / "src" / "firmware" / "usb" / "generic_hid" / "generic_hid_driver.cpp",
+            root / "generic_hid_driver.cpp",
             root / "tests" / "generic_hid_driver_test.cpp",
         ],
         ["SWITCH_PICO_HID_INSTANCE_COUNT=4"],

tests/test_prepare_bluepad32.py

@@ -1,194 +1,339 @@
-from __future__ import annotations
+"""
+Tests for prepare_bluepad32.py patch preparation tool.
+
+Tests cover:
+- Fresh patch application
+- Idempotence (second invocation succeeds without changing content)
+- Missing paths validation
+- Diverged/ambiguous repository states
+"""
 
-import shutil
 import subprocess
-import sys
-from pathlib import Path
-
+import tempfile
 import pytest
+from pathlib import Path
+from unittest.mock import patch as mock_patch
 
+import sys
 sys.path.insert(0, str(Path(__file__).parent.parent / "tools"))
 
-from prepare_bluepad32 import (  # noqa: E402
+from prepare_bluepad32 import (
     PatchError,
-    check_paths,
-    main,
-    prepare_bluepad32,
     resolve_paths,
+    check_paths,
+    is_patch_applied,
+    apply_patch,
+    prepare_bluepad32,
 )
 
 
-def run_git(repository: Path, *args: str) -> subprocess.CompletedProcess[str]:
-    return subprocess.run(
-        ["git", "-C", str(repository), *args],
+@pytest.fixture
+def temp_repo_structure():
+    """Create a temporary directory structure with git repositories."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        root = Path(tmpdir)
+        
+        # Create bluepad32 repo
+        bp_dir = root / "external" / "bluepad32"
+        bp_dir.mkdir(parents=True)
+        subprocess.run(["git", "init"], cwd=bp_dir, check=True, capture_output=True)
+        subprocess.run(["git", "config", "user.email", "test@example.com"], cwd=bp_dir, check=True, capture_output=True)
+        subprocess.run(["git", "config", "user.name", "Test User"], cwd=bp_dir, check=True, capture_output=True)
+        
+        # Create a file to patch
+        test_file = bp_dir / "test.txt"
+        test_file.write_text("line 1\n")
+        subprocess.run(["git", "add", "test.txt"], cwd=bp_dir, check=True, capture_output=True)
+        subprocess.run(["git", "commit", "-m", "initial"], cwd=bp_dir, check=True, capture_output=True)
+        
+        # Create patches dir
+        patches_dir = root / "patches"
+        patches_dir.mkdir()
+        
+        yield root, bp_dir, patches_dir
+
+
+def create_simple_patch(repo_path: Path, patch_path: Path, file_to_patch: str = "test.txt") -> str:
+    """
+    Create a simple patch file that modifies a file in the repository.
+    
+    Returns the patch content as a string.
+    """
+    # Create the modification
+    test_file = repo_path / file_to_patch
+    original_content = test_file.read_text()
+    modified_content = original_content + "line 2\n"
+    
+    # Generate patch using git diff
+    test_file.write_text(modified_content)
+    result = subprocess.run(
+        ["git", "diff", file_to_patch],
+        cwd=repo_path,
         capture_output=True,
         text=True,
         check=True,
     )
+    patch_content = result.stdout
+    
+    # Reset the file to original state
+    test_file.write_text(original_content)
+    
+    # Write patch to file
+    patch_path.write_text(patch_content)
+    return patch_content
 
 
-@pytest.fixture
-def bluepad32_fixture(tmp_path: Path) -> tuple[Path, Path, Path, Path]:
-    source = tmp_path / "external" / "bluepad32"
-    source.mkdir(parents=True)
-    run_git(source, "init")
-    run_git(source, "config", "user.email", "test@example.com")
-    run_git(source, "config", "user.name", "Test User")
-    (source / "test.txt").write_text("line 1\n", encoding="utf-8")
-    run_git(source, "add", "test.txt")
-    run_git(source, "commit", "-m", "initial")
-
-    patches = tmp_path / "patches"
-    patches.mkdir()
-    patch = patches / "bluepad32-sdl3-imu.patch"
-    original = (source / "test.txt").read_text(encoding="utf-8")
-    (source / "test.txt").write_text(f"{original}line 2\n", encoding="utf-8")
-    patch.write_text(run_git(source, "diff", "--", "test.txt").stdout, encoding="utf-8")
-    run_git(source, "restore", "test.txt")
-
-    output = tmp_path / "build-aio" / "_deps" / "bluepad32-src"
-    return tmp_path, source, patch, output
+def test_resolve_paths_with_defaults():
+    """Test that resolve_paths returns expected default paths."""
+    with tempfile.TemporaryDirectory() as tmpdir:
+        bp_path, patch_path = resolve_paths(Path(tmpdir))
+        assert bp_path == Path(tmpdir) / "external" / "bluepad32"
+        assert patch_path == Path(tmpdir) / "patches" / "bluepad32-sdl3-imu.patch"
 
 
-def source_status(source: Path) -> str:
-    return run_git(source, "status", "--porcelain", "--untracked-files=all").stdout
+def test_resolve_paths_no_root():
+    """Test resolve_paths with no root uses current directory."""
+    bp_path, patch_path = resolve_paths()
+    assert bp_path.is_absolute()
+    assert patch_path.is_absolute()
 
 
-def test_resolve_paths_uses_project_build_tree(tmp_path: Path) -> None:
-    source, patch, output = resolve_paths(tmp_path)
-
-    assert source == tmp_path / "external" / "bluepad32"
-    assert patch == tmp_path / "patches" / "bluepad32-sdl3-imu.patch"
-    assert output == tmp_path / "build" / "_deps" / "bluepad32-src"
-
-
-def test_check_paths_rejects_missing_source(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    shutil.rmtree(source)
-
+def test_check_paths_missing_bluepad32(temp_repo_structure):
+    """Test that check_paths fails if bluepad32 dir is missing."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    # Remove bluepad32
+    import shutil
+    shutil.rmtree(bp_dir)
+    
+    patch_file = patches_dir / "test.patch"
+    patch_file.write_text("dummy")
+    
     with pytest.raises(PatchError, match="bluepad32 directory does not exist"):
-        check_paths(source, patch, output)
+        check_paths(bp_dir, patch_file)
 
 
-def test_check_paths_rejects_missing_patch(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    patch.unlink()
-
+def test_check_paths_missing_patch(temp_repo_structure):
+    """Test that check_paths fails if patch file is missing."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "nonexistent.patch"
+    
     with pytest.raises(PatchError, match="patch file does not exist"):
-        check_paths(source, patch, output)
+        check_paths(bp_dir, patch_file)
 
 
-def test_check_paths_rejects_non_repository(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    shutil.rmtree(source / ".git")
-
+def test_check_paths_bluepad32_not_git_repo(temp_repo_structure):
+    """Test that check_paths fails if bluepad32 is not a git repo."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    # Remove .git to make it not a git repo
+    import shutil
+    shutil.rmtree(bp_dir / ".git")
+    
+    patch_file = patches_dir / "test.patch"
+    patch_file.write_text("dummy")
+    
     with pytest.raises(PatchError, match="not a git repository"):
-        check_paths(source, patch, output)
+        check_paths(bp_dir, patch_file)
 
 
-def test_check_paths_rejects_output_inside_source(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, _ = bluepad32_fixture
-
-    with pytest.raises(PatchError, match="outside the Bluepad32 source tree"):
-        check_paths(source, patch, source / "patched")
+def test_fresh_patch_application(temp_repo_structure):
+    """Test applying a fresh patch to a clean repository."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Verify test.txt before patch
+    test_file = bp_dir / "test.txt"
+    original = test_file.read_text()
+    assert "line 2" not in original
+    
+    # Apply patch
+    apply_patch(bp_dir, patch_file)
+    
+    # Verify test.txt after patch
+    patched = test_file.read_text()
+    assert "line 2" in patched
 
 
-def test_prepare_patches_copy_and_preserves_pristine_source(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-
-    result = prepare_bluepad32(source, patch, output)
-
-    assert result == output
-    assert (source / "test.txt").read_text(encoding="utf-8") == "line 1\n"
-    assert (output / "test.txt").read_text(encoding="utf-8") == "line 1\nline 2\n"
-    assert not (output / ".git").exists()
-    assert source_status(source) == ""
+def test_idempotent_patch_application(temp_repo_structure):
+    """Test that applying the same patch twice succeeds (idempotence)."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # First application
+    apply_patch(bp_dir, patch_file)
+    test_file = bp_dir / "test.txt"
+    after_first = test_file.read_text()
+    
+    # Second application should succeed without changing content
+    apply_patch(bp_dir, patch_file)
+    after_second = test_file.read_text()
+    
+    assert after_first == after_second
 
 
-def test_prepare_replaces_existing_output_idempotently(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    prepare_bluepad32(source, patch, output)
-    (output / "stale.txt").write_text("stale", encoding="utf-8")
-
-    prepare_bluepad32(source, patch, output)
-
-    assert not (output / "stale.txt").exists()
-    assert (output / "test.txt").read_text(encoding="utf-8") == "line 1\nline 2\n"
-    assert source_status(source) == ""
+def test_is_patch_applied_not_applied(temp_repo_structure):
+    """Test is_patch_applied returns False for unapplied patch."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Patch not applied yet
+    assert is_patch_applied(bp_dir, patch_file) is False
 
 
-def test_prepare_rejects_dirty_source_without_replacing_output(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    output.mkdir(parents=True)
-    sentinel = output / "sentinel.txt"
-    sentinel.write_text("keep", encoding="utf-8")
-    (source / "test.txt").write_text("local edit\n", encoding="utf-8")
-
-    with pytest.raises(PatchError, match="must be pristine"):
-        prepare_bluepad32(source, patch, output)
-
-    assert sentinel.read_text(encoding="utf-8") == "keep"
+def test_is_patch_applied_already_applied(temp_repo_structure):
+    """Test is_patch_applied returns True for already applied patch."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Apply patch first
+    apply_patch(bp_dir, patch_file)
+    
+    # Now check should detect it's applied
+    assert is_patch_applied(bp_dir, patch_file) is True
 
 
-def test_prepare_rejects_diverged_source_revision(
-    bluepad32_fixture: tuple[Path, Path, Path, Path],
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    (source / "test.txt").write_text("different base\n", encoding="utf-8")
-    run_git(source, "add", "test.txt")
-    run_git(source, "commit", "-m", "diverge")
-
+def test_diverged_repository_state(temp_repo_structure):
+    """Test that diverged repository (patch doesn't apply cleanly) is rejected."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Diverge the repository by modifying the file such that the patch conflicts
+    test_file = bp_dir / "test.txt"
+    test_file.write_text("completely different line 1\n")
+    subprocess.run(["git", "add", "test.txt"], cwd=bp_dir, check=True, capture_output=True)
+    subprocess.run(["git", "commit", "-m", "divergence"], cwd=bp_dir, check=True, capture_output=True)
+    
+    # Try to apply patch - should fail because file content doesn't match
     with pytest.raises(PatchError, match="Patch validation failed"):
-        prepare_bluepad32(source, patch, output)
-
-    assert not output.exists()
+        apply_patch(bp_dir, patch_file)
 
 
-def test_prepare_uses_default_paths(
-    bluepad32_fixture: tuple[Path, Path, Path, Path], monkeypatch: pytest.MonkeyPatch
-) -> None:
-    root, source, _, _ = bluepad32_fixture
-    monkeypatch.chdir(root)
-
-    output = prepare_bluepad32()
-
-    assert output == root / "build" / "_deps" / "bluepad32-src"
-    assert (output / "test.txt").read_text(encoding="utf-8") == "line 1\nline 2\n"
-    assert source_status(source) == ""
+def test_missing_bluepad32_path(temp_repo_structure):
+    """Test prepare_bluepad32 fails gracefully with missing bluepad32."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    import shutil
+    shutil.rmtree(bp_dir)
+    
+    patch_file = patches_dir / "test.patch"
+    patch_file.write_text("dummy")
+    
+    with pytest.raises(PatchError, match="bluepad32 directory does not exist"):
+        prepare_bluepad32(bp_dir, patch_file)
 
 
-def test_cli_accepts_explicit_output(
-    bluepad32_fixture: tuple[Path, Path, Path, Path], monkeypatch: pytest.MonkeyPatch
-) -> None:
-    _, source, patch, output = bluepad32_fixture
-    monkeypatch.setattr(
-        sys,
-        "argv",
-        [
-            "prepare_bluepad32.py",
-            "--bluepad32",
-            str(source),
-            "--patch",
-            str(patch),
-            "--output",
-            str(output),
-        ],
-    )
+def test_missing_patch_file(temp_repo_structure):
+    """Test prepare_bluepad32 fails gracefully with missing patch file."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "nonexistent.patch"
+    
+    with pytest.raises(PatchError, match="patch file does not exist"):
+        prepare_bluepad32(bp_dir, patch_file)
 
-    assert main() == 0
-    assert (output / "test.txt").read_text(encoding="utf-8") == "line 1\nline 2\n"
-    assert source_status(source) == ""
+
+def test_prepare_bluepad32_full_workflow(temp_repo_structure):
+    """Test complete prepare_bluepad32 workflow: apply then idempotent re-apply."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    test_file = bp_dir / "test.txt"
+    original = test_file.read_text()
+    
+    # First prepare (should apply patch)
+    prepare_bluepad32(bp_dir, patch_file)
+    after_first = test_file.read_text()
+    assert after_first != original
+    assert "line 2" in after_first
+    
+    # Second prepare (should be idempotent)
+    prepare_bluepad32(bp_dir, patch_file)
+    after_second = test_file.read_text()
+    assert after_first == after_second
+
+
+def test_prepare_bluepad32_with_defaults(temp_repo_structure):
+    """Test prepare_bluepad32 uses correct defaults when paths not provided."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "bluepad32-sdl3-imu.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Change to root directory and call with defaults
+    import os
+    original_cwd = os.getcwd()
+    try:
+        os.chdir(root)
+        prepare_bluepad32()  # Use defaults
+    finally:
+        os.chdir(original_cwd)
+    
+    # Verify patch was applied
+    test_file = bp_dir / "test.txt"
+    assert "line 2" in test_file.read_text()
+
+
+def test_patch_application_with_conflicting_content(temp_repo_structure):
+    """Test that patch with conflicting content is rejected."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    # Create a patch that adds a specific change
+    patch_content = """--- a/test.txt
++++ b/test.txt
+@@ -1 +1,3 @@
+ line 1
++line 2
++line 3
+"""
+    
+    patch_file = patches_dir / "conflict.patch"
+    patch_file.write_text(patch_content)
+    
+    # Modify the file to have different content that won't match the patch context
+    test_file = bp_dir / "test.txt"
+    test_file.write_text("modified line 1\n")
+    subprocess.run(["git", "add", "test.txt"], cwd=bp_dir, check=True, capture_output=True)
+    subprocess.run(["git", "commit", "-m", "modify"], cwd=bp_dir, check=True, capture_output=True)
+    
+    # Try to apply patch - should fail due to context mismatch
+    with pytest.raises(PatchError):
+        apply_patch(bp_dir, patch_file)
+
+
+def test_cli_with_explicit_paths(temp_repo_structure):
+    """Test CLI argument parsing with explicit paths."""
+    root, bp_dir, patches_dir = temp_repo_structure
+    
+    patch_file = patches_dir / "test.patch"
+    create_simple_patch(bp_dir, patch_file, "test.txt")
+    
+    # Simulate CLI call
+    sys.argv = [
+        "prepare_bluepad32.py",
+        "--bluepad32", str(bp_dir),
+        "--patch", str(patch_file),
+    ]
+    
+    from prepare_bluepad32 import main
+    
+    # Should not raise
+    try:
+        main()
+    except SystemExit as e:
+        # main() calls sys.exit on success, which we need to catch
+        if e.code != 0:
+            raise

tests/test_profile_service_native.py

@@ -18,12 +18,12 @@ def test_profile_service_native(tmp_path: Path) -> None:
             "-Werror",
             "-pedantic",
             f"-I{root / 'tests' / 'bluepad32_native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "profile_service_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
-            str(root / "src" / "firmware" / "profile" / "profile_storage.cpp"),
-            str(root / "src" / "firmware" / "profile" / "profile_service.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
+            str(root / "profile_storage.cpp"),
+            str(root / "profile_service.cpp"),
             "-o",
             str(executable),
         ],

tests/test_profile_storage_native.py

@@ -17,11 +17,11 @@ def test_profile_storage_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "profile_storage_test.cpp"),
-            str(root / "src" / "firmware" / "core" / "controller_identity.cpp"),
-            str(root / "src" / "firmware" / "profile" / "controller_profile.cpp"),
-            str(root / "src" / "firmware" / "profile" / "profile_storage.cpp"),
+            str(root / "controller_identity.cpp"),
+            str(root / "controller_profile.cpp"),
+            str(root / "profile_storage.cpp"),
             "-o",
             str(executable),
         ],

tests/test_switch_haptics_native.py

@@ -19,8 +19,8 @@ def test_switch_haptics_native(tmp_path: Path) -> None:
             "-Wextra",
             "-Werror",
             "-pedantic",
-            f"-I{root / 'src' / 'firmware'}",
-            str(root / "src" / "firmware" / "usb" / "switch" / "switch_haptics.cpp"),
+            f"-I{root}",
+            str(root / "switch_haptics.cpp"),
             str(root / "tests" / "switch_haptics_test.cpp"),
             "-o",
             str(executable),

tests/test_switch_pro_descriptors_native.py

@@ -25,7 +25,7 @@ def compile_descriptor_test(
         command.append(f"-DSWITCH_PICO_HID_INSTANCE_COUNT={configured_count}")
     command.extend(
         [
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "switch_pro_descriptors_test.cpp"),
             "-o",
             str(output),

tests/test_switch_pro_driver_context_native.py

@@ -21,10 +21,10 @@ def test_switch_pro_driver_four_contexts_native(tmp_path: Path) -> None:
             "-pedantic",
             "-DSWITCH_PICO_HID_INSTANCE_COUNT=4",
             f"-I{root / 'tests' / 'native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
-            str(root / "src" / "firmware" / "usb" / "switch" / "switch_pro_driver.cpp"),
-            str(root / "src" / "firmware" / "usb" / "usb_output_driver.cpp"),
-            str(root / "src" / "firmware" / "usb" / "switch" / "switch_haptics.cpp"),
+            f"-I{root}",
+            str(root / "switch_pro_driver.cpp"),
+            str(root / "usb_output_driver.cpp"),
+            str(root / "switch_haptics.cpp"),
             str(root / "tests" / "switch_pro_driver_context_test.cpp"),
             "-o",
             str(executable),

tests/test_usb_configuration_management_native.py

@@ -19,7 +19,7 @@ def test_usb_configuration_management_native(tmp_path: Path) -> None:
             "-Werror",
             "-pedantic",
             f"-I{root / 'tests' / 'usb_management_native_stubs'}",
-            f"-I{root / 'src' / 'firmware'}",
+            f"-I{root}",
             str(root / "tests" / "usb_configuration_management_test.cpp"),
             "-o",
             str(executable),

tests/test_usb_output_driver_native.py

@@ -36,13 +36,13 @@ def test_usb_output_driver_contracts(tmp_path: Path) -> None:
                     "-DSWITCH_PICO_USB_OUTPUT_MODES=1",
                     *backend_definitions,
                     f"-I{root / 'tests' / 'native_stubs'}",
-                    f"-I{root / 'src' / 'firmware'}",
+                    f"-I{root}",
                     str(root / "tests" / "usb_output_driver_test.cpp"),
-                    str(root / "src" / "firmware" / "usb" / "switch" / "switch_pro_driver.cpp"),
-                    str(root / "src" / "firmware" / "usb" / "usb_output_driver.cpp"),
-                    str(root / "src" / "firmware" / "usb" / "generic_hid" / "generic_hid_driver.cpp"),
-                    str(root / "src" / "firmware" / "usb" / "xinput" / "xinput_driver.cpp"),
-                    str(root / "src" / "firmware" / "usb" / "switch" / "switch_haptics.cpp"),
+                    str(root / "switch_pro_driver.cpp"),
+                    str(root / "usb_output_driver.cpp"),
+                    str(root / "generic_hid_driver.cpp"),
+                    str(root / "xinput_driver.cpp"),
+                    str(root / "switch_haptics.cpp"),
                     "-o",
                     str(executable),
                 ],

tests/usb_configuration_management_test.cpp

@@ -1,11 +1,12 @@
-#include "usb/usb_configuration_management.h"
+#include "usb_configuration_management.h"
+
 #include <cstdlib>
 #include <cstring>
 #include <iostream>
 #include <vector>
 
 #include <tusb.h>
-#include "usb/usb_output_driver.h"
+#include "usb_output_driver.h"
 
 namespace {
 
@@ -787,10 +788,10 @@ bool tud_control_status(uint8_t, const tusb_control_request_t*) {
     return true;
 }
 
-#include "configuration/adapter_configuration.cpp"
-#include "core/controller_identity.cpp"
-#include "profile/controller_profile.cpp"
-#include "usb/usb_configuration_management.cpp"
+#include "../adapter_configuration.cpp"
+#include "../controller_identity.cpp"
+#include "../controller_profile.cpp"
+#include "../usb_configuration_management.cpp"
 
 int main() {
     current_configuration.state = ConfigurationServiceState::kReady;

tests/usb_output_driver_test.cpp

@@ -4,17 +4,17 @@
 #include <cstring>
 #include <iostream>
 
-#include "adapter/adapter_host_probe_state.h"
-#include "usb/generic_hid/generic_hid_descriptors.h"
-#include "usb/generic_hid/generic_hid_driver.h"
-#include "usb/xinput/xinput_descriptors.h"
-#include "usb/xinput/xinput_protocol.h"
+#include "adapter_host_probe_state.h"
+#include "generic_hid_descriptors.h"
+#include "generic_hid_driver.h"
+#include "xinput_descriptors.h"
+#include "xinput_protocol.h"
 #include "device/usbd_pvt.h"
 #include "pico/time.h"
-#include "usb/switch/switch_pro_driver.h"
+#include "switch_pro_driver.h"
 #include "tusb.h"
-#include "usb/usb_output_driver.h"
-#include "usb/xinput/xinput_driver.h"
+#include "usb_output_driver.h"
+#include "xinput_driver.h"
 
 namespace {
 

tools/prepare_bluepad32.py

@@ -1,9 +1,8 @@
 #!/usr/bin/env python3
-"""Create a patched build-local copy of the pinned Bluepad32 source."""
+"""Apply the project Bluepad32 patch exactly once."""
 from __future__ import annotations
 
 import argparse
-import shutil
 import subprocess
 import sys
 from pathlib import Path
@@ -13,125 +12,69 @@ class PatchError(RuntimeError):
     pass
 
 
-def resolve_paths(repo_root: Path | None = None) -> tuple[Path, Path, Path]:
+def resolve_paths(repo_root: Path | None = None) -> tuple[Path, Path]:
     root = Path.cwd() if repo_root is None else Path(repo_root)
     return (
         root / "external" / "bluepad32",
         root / "patches" / "bluepad32-sdl3-imu.patch",
-        root / "build" / "_deps" / "bluepad32-src",
     )
 
 
-def _run(command: list[str], *, cwd: Path | None = None) -> subprocess.CompletedProcess[str]:
+def check_paths(bluepad32_path: Path, patch_path: Path) -> None:
+    if not bluepad32_path.is_dir():
+        raise PatchError(f"bluepad32 directory does not exist: {bluepad32_path}")
+    if not (bluepad32_path / ".git").exists():
+        raise PatchError(f"Bluepad32 is not a git repository: {bluepad32_path}")
+    if not patch_path.is_file():
+        raise PatchError(f"patch file does not exist: {patch_path}")
+
+
+def git_apply(bluepad32_path: Path, patch_path: Path, *args: str) -> subprocess.CompletedProcess[str]:
     return subprocess.run(
-        command,
-        cwd=cwd,
+        ["git", "-C", str(bluepad32_path), "apply", *args, str(patch_path)],
         capture_output=True,
         text=True,
         check=False,
     )
 
 
-def check_paths(source_path: Path, patch_path: Path, output_path: Path) -> None:
-    if not source_path.is_dir():
-        raise PatchError(f"bluepad32 directory does not exist: {source_path}")
-    if not patch_path.is_file():
-        raise PatchError(f"patch file does not exist: {patch_path}")
-
-    repository_check = _run(
-        ["git", "-C", str(source_path), "rev-parse", "--is-inside-work-tree"]
-    )
-    if repository_check.returncode != 0:
-        raise PatchError(f"Bluepad32 is not a git repository: {source_path}")
-
-    source = source_path.resolve()
-    output = output_path.resolve()
-    if output == source or source in output.parents:
-        raise PatchError("patched output must be outside the Bluepad32 source tree")
+def is_patch_applied(bluepad32_path: Path, patch_path: Path) -> bool:
+    return git_apply(bluepad32_path, patch_path, "--reverse", "--check").returncode == 0
 
 
-def validate_pristine_source(source_path: Path, patch_path: Path) -> None:
-    status = _run(
-        [
-            "git",
-            "-C",
-            str(source_path),
-            "status",
-            "--porcelain",
-            "--untracked-files=all",
-        ]
-    )
-    if status.returncode != 0:
-        detail = status.stderr.strip() or "git status failed"
-        raise PatchError(f"Could not inspect Bluepad32 source: {detail}")
-    if status.stdout.strip():
-        raise PatchError(
-            "Bluepad32 source must be pristine; patches are applied only to the build-local copy"
-        )
+def apply_patch(bluepad32_path: Path, patch_path: Path) -> None:
+    if is_patch_applied(bluepad32_path, patch_path):
+        return
 
-    check = _run(
-        ["git", "-C", str(source_path), "apply", "--check", str(patch_path)]
-    )
+    check = git_apply(bluepad32_path, patch_path, "--check")
     if check.returncode != 0:
         detail = check.stderr.strip() or "patch does not apply"
-        raise PatchError(f"Patch validation failed (source revision may have diverged):\n{detail}")
+        raise PatchError(f"Patch validation failed (repository may be diverged):\n{detail}")
 
-
-def _copy_and_patch(source_path: Path, patch_path: Path, output_path: Path) -> None:
-    output_path.parent.mkdir(parents=True, exist_ok=True)
-    staging_path = output_path.with_name(f".{output_path.name}.tmp")
-
-    if staging_path.exists():
-        shutil.rmtree(staging_path)
-
-    try:
-        shutil.copytree(
-            source_path,
-            staging_path,
-            symlinks=True,
-            ignore=shutil.ignore_patterns(".git"),
-        )
-        result = _run(
-            ["git", "apply", "--no-index", str(patch_path.resolve())],
-            cwd=staging_path,
-        )
-        if result.returncode != 0:
-            detail = result.stderr.strip() or "git apply failed"
-            raise PatchError(f"Could not patch build-local Bluepad32 copy: {detail}")
-
-        if output_path.exists():
-            shutil.rmtree(output_path)
-        staging_path.replace(output_path)
-    except Exception:
-        if staging_path.exists():
-            shutil.rmtree(staging_path)
-        raise
+    result = git_apply(bluepad32_path, patch_path)
+    if result.returncode != 0:
+        detail = result.stderr.strip() or "git apply failed"
+        raise PatchError(f"Could not patch Bluepad32: {detail}")
 
 
 def prepare_bluepad32(
-    source_path: Path | None = None,
+    bluepad32_path: Path | None = None,
     patch_path: Path | None = None,
-    output_path: Path | None = None,
-) -> Path:
-    default_source, default_patch, default_output = resolve_paths()
-    source = Path(source_path or default_source)
+) -> None:
+    default_bluepad32, default_patch = resolve_paths()
+    dependency = Path(bluepad32_path or default_bluepad32)
     patch = Path(patch_path or default_patch)
-    output = Path(output_path or default_output)
-
-    check_paths(source, patch, output)
-    validate_pristine_source(source, patch)
-    _copy_and_patch(source, patch, output)
-    return output
+    check_paths(dependency, patch)
+    apply_patch(dependency, patch)
 
 
 def main() -> int:
     parser = argparse.ArgumentParser(description=__doc__)
     parser.add_argument("--bluepad32", type=Path)
     parser.add_argument("--patch", type=Path)
-    parser.add_argument("--output", type=Path)
     args = parser.parse_args()
     try:
-        prepare_bluepad32(args.bluepad32, args.patch, args.output)
+        prepare_bluepad32(args.bluepad32, args.patch)
     except PatchError as exc:
         print(f"error: {exc}", file=sys.stderr)
         return 1

usb_configuration_management.cpp

@@ -1,12 +1,13 @@
-#include "usb/usb_configuration_management.h"
+#include "usb_configuration_management.h"
+
 #include <string.h>
 
-#include "configuration/adapter_configuration.h"
-#include "adapter/adapter_host_probe.h"
-#include "adapter/adapter_reboot.h"
-#include "adapter/adapter_usb_mode.h"
+#include "adapter_configuration.h"
+#include "adapter_host_probe.h"
+#include "adapter_reboot.h"
+#include "adapter_usb_mode.h"
 #include "tusb.h"
-#include "usb/usb_output_driver.h"
+#include "usb_output_driver.h"
 
 namespace UsbConfigurationManagement {
 namespace {

usb_configuration_management.h

@@ -5,9 +5,9 @@
 
 #include "tusb.h"
 
-#include "input/bluepad32_input_backend.h"
-#include "configuration/configuration_service.h"
-#include "profile/profile_service.h"
+#include "bluepad32_input_backend.h"
+#include "configuration_service.h"
+#include "profile_service.h"
 
 namespace UsbConfigurationManagement {
 

usb_output_driver.cpp

@@ -1,23 +1,23 @@
-#include "usb/usb_output_driver.h"
+#include "usb_output_driver.h"
 
 #include <cstring>
 #include <stdio.h>
 
 #include "device/usbd_pvt.h"
-#include "usb/switch/switch_pro_driver.h"
-#include "usb/switch/switch_pro_descriptors.h"
+#include "switch_pro_driver.h"
+#include "switch_pro_descriptors.h"
 #include "tusb.h"
 
 #ifdef SWITCH_PICO_BLUEPAD32
-#include "usb/usb_configuration_management.h"
+#include "usb_configuration_management.h"
 #endif
 
 #ifdef SWITCH_PICO_USB_OUTPUT_MODES
-#include "adapter/adapter_host_probe.h"
-#include "usb/generic_hid/generic_hid_descriptors.h"
-#include "usb/generic_hid/generic_hid_driver.h"
-#include "usb/xinput/xinput_descriptors.h"
-#include "usb/xinput/xinput_driver.h"
+#include "adapter_host_probe.h"
+#include "generic_hid_descriptors.h"
+#include "generic_hid_driver.h"
+#include "xinput_descriptors.h"
+#include "xinput_driver.h"
 #endif
 
 #ifdef SWITCH_PICO_LOG

usb_output_driver.h

@@ -2,9 +2,9 @@
 
 #include <stdint.h>
 
-#include "adapter/adapter_usb_mode.h"
-#include "core/controller_state.h"
-#include "usb/switch/switch_haptics.h"
+#include "adapter_usb_mode.h"
+#include "controller_state.h"
+#include "switch_haptics.h"
 
 // Mode capability bits published in USB management info. Input is present in
 // every current mode; rumble/motion describe host-visible USB capabilities.