Fix Docker macOS timestamp issues and improve build reproducibility

- Add rsync-based source sync for Docker builds to fix macOS VirtioFS
  timestamp inconsistencies that caused autoconf sanity checks to fail
- Add config.sub wrapper (SHELL/CONFIG_SHELL) to support emscripten/wasm32
  targets without modifying submodule files
- Fix protobuf build to use native gcc/g++ for protoc instead of Emscripten
- Add python PATH fix for macOS (Homebrew's python3 symlink) in wxWidgets build

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

docker/Dockerfile

@@ -18,6 +18,7 @@ RUN apt-get update && apt-get install -y \
     swig \
     unixodbc-dev \
     ccache \
+    rsync \
     && rm -rf /var/lib/apt/lists/*
 
 # Configure ccache for Emscripten

docker/build.sh

@@ -20,6 +20,12 @@ fi
 # Start container if not running
 docker compose -f docker/docker-compose.yml up -d
 
+# Sync source code to container volume (fixes macOS Docker timestamp issues)
+# This ensures timestamps are consistent within the container filesystem
+echo "Syncing source code to container..."
+docker compose -f docker/docker-compose.yml exec kicad-wasm-builder \
+    rsync -a --delete --exclude='build-wasm' --exclude='output' /workspace-host/ /workspace/
+
 # Run build command (without asyncify - handled on host due to memory requirements)
 docker compose -f docker/docker-compose.yml exec kicad-wasm-builder \
     /workspace/scripts/kicad/build-pcbnew.sh "${ARGS[@]}"

docker/docker-compose.yml

@@ -13,8 +13,11 @@ services:
           memory: 32G
 
     volumes:
-      # Source code (read-only - all modifications happen in build-wasm volume)
-      - ..:/workspace:ro
+      # Host source mounted read-only at staging location
+      # (rsync'd to /workspace on container start to fix macOS timestamp issues)
+      - ..:/workspace-host:ro
+      # Synced source in Docker volume (consistent timestamps)
+      - workspace-src:/workspace
       # Named volume for build cache (faster than bind mount on macOS)
       - kicad-build-cache:/workspace/build-wasm
       # Output directory for easy access to final WASM files
@@ -26,3 +29,4 @@ services:
 
 volumes:
   kicad-build-cache:
+  workspace-src:

docker/entrypoint.sh

@@ -4,5 +4,17 @@ set -e
 # Source Emscripten environment
 source /emsdk/emsdk_env.sh 2>/dev/null
 
+# Sync source from host to workspace volume
+# This fixes macOS Docker timestamp issues with bind mounts
+# (autoconf sanity checks fail when timestamps appear inconsistent)
+if [[ -d /workspace-host ]]; then
+    echo "Syncing source code to container volume..."
+    rsync -a --delete \
+        --exclude='build-wasm' \
+        --exclude='output' \
+        /workspace-host/ /workspace/
+    echo "Sync complete."
+fi
+
 # Execute command or start shell
 exec "$@"