diff --git a/docker/build.sh b/docker/build.sh
index d78f4f1..ea65a2e 100755
--- a/docker/build.sh
+++ b/docker/build.sh
@@ -14,6 +14,6 @@ docker compose -f docker/docker-compose.yml exec kicad-wasm-builder \
 # Copy output to host-accessible directory
 echo "Copying build output to ./output/..."
 docker compose -f docker/docker-compose.yml exec kicad-wasm-builder \
-    bash -c "mkdir -p /workspace/output && cp -r /workspace/build-wasm/kicad-pcbnew/bin/* /workspace/output/ 2>/dev/null || true"
+    bash -c "mkdir -p /workspace/output && cp /workspace/build-wasm/kicad-pcbnew/pcbnew/pcbnew.{js,wasm,wasm.map,worker.js} /workspace/output/ 2>/dev/null || cp /workspace/build-wasm/kicad-pcbnew/pcbnew/pcbnew.{js,wasm} /workspace/output/"
 
 echo "Build complete. Output files in ./output/"
diff --git a/docker/docker-compose.yml b/docker/docker-compose.yml
index 6e4f34b..4ee37f3 100644
--- a/docker/docker-compose.yml
+++ b/docker/docker-compose.yml
@@ -13,8 +13,8 @@ services:
           memory: 32G
 
     volumes:
-      # Source code (read-write for git operations)
-      - ..:/workspace:cached
+      # Source code (read-only - all modifications happen in build-wasm volume)
+      - ..:/workspace:ro
       # 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
diff --git a/scripts/build-wxuniversal-wasm.sh b/scripts/build-wxuniversal-wasm.sh
index 8e702ec..8a9629b 100755
--- a/scripts/build-wxuniversal-wasm.sh
+++ b/scripts/build-wxuniversal-wasm.sh
@@ -59,7 +59,7 @@ cd "$BUILD_DIR"
 # --enable-universal         Use wxUniversal (draws widgets directly)
 # --disable-shared           Build static libraries
 # --with-opengl              Enable OpenGL/WebGL support
-# --disable-exceptions       Emscripten doesn't support C++ exceptions well
+# --enable-exceptions        Enable C++ exceptions (needed for KiCad debug builds)
 # --disable-richtext         Not needed for KiCad, simplifies build
 # --without-libtiff          Avoid external dependencies
 # --disable-xlocale          Browser environment handles locale
@@ -83,8 +83,8 @@ else
     echo "Building wxWidgets in RELEASE mode"
 fi
 
-export CFLAGS="-DZ_HAVE_UNISTD_H=1 ${WX_DEBUG_FLAGS}"
-export CXXFLAGS="-DZ_HAVE_UNISTD_H=1 -I$PCRE2_INCLUDE ${WX_DEBUG_FLAGS}"
+export CFLAGS="-DZ_HAVE_UNISTD_H=1 ${WX_DEBUG_FLAGS} -fexceptions -pthread -matomics -mbulk-memory"
+export CXXFLAGS="-DZ_HAVE_UNISTD_H=1 -I$PCRE2_INCLUDE ${WX_DEBUG_FLAGS} -fexceptions -pthread -matomics -mbulk-memory"
 
 emconfigure "$WX_SOURCE/configure" \
     --host=emscripten \
@@ -92,7 +92,7 @@ emconfigure "$WX_SOURCE/configure" \
     --enable-universal \
     --disable-shared \
     --with-opengl \
-    --disable-exceptions \
+    --enable-exceptions \
     --disable-richtext \
     --without-libtiff \
     --disable-xlocale \
diff --git a/scripts/deps/build-all-deps.sh b/scripts/deps/build-all-deps.sh
index 581ce10..f4a651e 100755
--- a/scripts/deps/build-all-deps.sh
+++ b/scripts/deps/build-all-deps.sh
@@ -43,6 +43,7 @@ log_info "=== Phase 1: Header-only libraries ==="
 log_info "=== Phase 2: Basic compression/serialization ==="
 "${SCRIPT_DIR}/build-zstd.sh" ${CLEAN}
 "${SCRIPT_DIR}/build-protobuf.sh" ${CLEAN}
+"${SCRIPT_DIR}/build-boost.sh" ${CLEAN}
 
 # 3. Font rendering stack
 log_info "=== Phase 3: Font rendering ==="
@@ -54,6 +55,11 @@ log_info "=== Phase 4: Graphics libraries ==="
 "${SCRIPT_DIR}/build-pixman.sh" ${CLEAN}
 "${SCRIPT_DIR}/build-cairo.sh" ${CLEAN}
 
+# 4b. Stub headers (needed for KiCad compilation but functionality is stubbed)
+log_info "=== Phase 4b: Stub dependencies (headers only) ==="
+"${SCRIPT_DIR}/build-curl-headers.sh" ${CLEAN}
+"${SCRIPT_DIR}/build-libgit2-headers.sh" ${CLEAN}
+
 # 5. Optional heavy dependencies
 if [ $WITH_OCC -eq 1 ]; then
     log_info "=== Phase 5a: OpenCASCADE (3D/STEP support) ==="
diff --git a/scripts/deps/build-boost.sh b/scripts/deps/build-boost.sh
index 95e1e65..8905e79 100755
--- a/scripts/deps/build-boost.sh
+++ b/scripts/deps/build-boost.sh
@@ -76,7 +76,7 @@ fi
 cat > user-config.jam << EOF
 using clang : emscripten
     : em++
-    : <cxxflags>"${BOOST_DEBUG_FLAGS} -pthread"
+    : <cxxflags>"${BOOST_DEBUG_FLAGS} -pthread -matomics -mbulk-memory"
       <linkflags>"-pthread"
     ;
 EOF
@@ -94,7 +94,7 @@ log_info "Building Boost.Locale (${BOOST_VARIANT})..."
     link=static \
     threading=multi \
     runtime-link=static \
-    cxxflags="${BOOST_DEBUG_FLAGS} -pthread" \
+    cxxflags="${BOOST_DEBUG_FLAGS} -pthread -matomics -mbulk-memory" \
     install
 
 create_stamp "${BOOST_STAMP}"
diff --git a/scripts/deps/build-cairo.sh b/scripts/deps/build-cairo.sh
index e0721c3..fe41133 100755
--- a/scripts/deps/build-cairo.sh
+++ b/scripts/deps/build-cairo.sh
@@ -82,15 +82,19 @@ cpu = 'wasm32'
 endian = 'little'
 
 [properties]
-# Prevent finding system libraries when cross-compiling
-sys_root = '${SYSROOT}'
+# Don't set sys_root - it gets prepended to pkg-config paths which are already absolute
+# Just use pkg_config_libdir to control where we find .pc files
 pkg_config_libdir = '${SYSROOT}/lib/pkgconfig'
 
 [built-in options]
 default_library = 'static'
 b_staticpic = false
 b_pie = false
-c_args = [${MESON_DEBUG_FLAGS}, '-pthread', '-I${SYSROOT}/include', '-I${SYSROOT}/include/freetype2', '-I${SYSROOT}/include/pixman-1']
+# Emscripten has these functions but meson checks fail - provide HAVE_ defines
+# to prevent Cairo from defining its own conflicting implementations
+# Include ft2build.h and ftcolor.h to fix FT_Color forward declaration bug in cairo-ft-private.h
+# (the forward declaration is inside HAVE_FT_SVG_DOCUMENT but used in HAVE_FT_COLR_V1)
+c_args = [${MESON_DEBUG_FLAGS}, '-pthread', '-matomics', '-mbulk-memory', '-I${SYSROOT}/include', '-I${SYSROOT}/include/freetype2', '-I${SYSROOT}/include/pixman-1', '-DHAVE_CTIME_R=1', '-DHAVE_LOCALTIME_R=1', '-DHAVE_GMTIME_R=1', '-DHAVE_STRNDUP=1', '-include', 'ft2build.h', '-include', 'freetype/ftcolor.h']
 c_link_args = ['-pthread', '-L${SYSROOT}/lib']
 pkg_config_path = '${SYSROOT}/lib/pkgconfig'
 EOF
@@ -119,8 +123,38 @@ meson setup "${CAIRO_DIR}" \
     -Dlibpng:default_library=static
 
 # JOBS is set in env.sh (default: 1 for sequential builds, use -j N to override)
-ninja -j${JOBS}
-ninja install
+# Build only the library targets we need - utility executables fail to link and aren't needed
+ninja -j${JOBS} src/libcairo.a
+
+# Manual installation - ninja install tries to build everything including utilities
+# which fail due to freetype atomics issues
+log_info "Installing Cairo library and headers..."
+mkdir -p "${SYSROOT}/lib" "${SYSROOT}/include/cairo" "${SYSROOT}/lib/pkgconfig"
+cp src/libcairo.a "${SYSROOT}/lib/"
+cp "${CAIRO_DIR}/src/cairo.h" "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-deprecated.h" "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-version.h" "${SYSROOT}/include/cairo/"
+# cairo-features.h is generated during configure in the build directory
+cp src/cairo-features.h "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-ft.h" "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-pdf.h" "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-ps.h" "${SYSROOT}/include/cairo/"
+cp "${CAIRO_DIR}/src/cairo-script.h" "${SYSROOT}/include/cairo/"
+
+# Create pkg-config file
+cat > "${SYSROOT}/lib/pkgconfig/cairo.pc" << PKGEOF
+prefix=${SYSROOT}
+exec_prefix=\${prefix}
+libdir=\${prefix}/lib
+includedir=\${prefix}/include
+
+Name: cairo
+Description: Multi-platform 2D graphics library
+Version: 1.18.0
+Libs: -L\${libdir} -lcairo
+Cflags: -I\${includedir}/cairo
+Requires.private: freetype2 pixman-1
+PKGEOF
 
 create_stamp "${CAIRO_STAMP}"
 log_info "Cairo build complete!"
diff --git a/scripts/deps/build-freetype.sh b/scripts/deps/build-freetype.sh
index 6a433bc..4a459a5 100755
--- a/scripts/deps/build-freetype.sh
+++ b/scripts/deps/build-freetype.sh
@@ -56,8 +56,8 @@ emcmake cmake "${FREETYPE_DIR}" \
     -DCMAKE_BUILD_TYPE=${BUILD_TYPE:-Debug} \
     -DCMAKE_INSTALL_PREFIX="${SYSROOT}" \
     -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
-    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0}" \
-    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0}" \
+    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
+    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
     -DFT_DISABLE_BZIP2=ON \
     -DFT_DISABLE_BROTLI=ON \
     -DFT_DISABLE_HARFBUZZ=ON \
@@ -68,5 +68,12 @@ emcmake cmake "${FREETYPE_DIR}" \
 emmake make -j${JOBS}
 emmake make install
 
+# Create symlink without debug suffix for pkg-config compatibility
+# FreeType CMake adds 'd' suffix for Debug builds but pkg-config expects 'libfreetype'
+if [ -f "${SYSROOT}/lib/libfreetyped.a" ] && [ ! -f "${SYSROOT}/lib/libfreetype.a" ]; then
+    ln -sf libfreetyped.a "${SYSROOT}/lib/libfreetype.a"
+    log_info "Created libfreetype.a symlink for pkg-config"
+fi
+
 create_stamp "${FREETYPE_STAMP}"
 log_info "FreeType build complete!"
diff --git a/scripts/deps/build-harfbuzz.sh b/scripts/deps/build-harfbuzz.sh
index 165116d..02ddba3 100755
--- a/scripts/deps/build-harfbuzz.sh
+++ b/scripts/deps/build-harfbuzz.sh
@@ -60,8 +60,8 @@ emcmake cmake "${HARFBUZZ_DIR}" \
     -DCMAKE_BUILD_TYPE=${BUILD_TYPE:-Debug} \
     -DCMAKE_INSTALL_PREFIX="${SYSROOT}" \
     -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
-    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0}" \
-    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0}" \
+    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
+    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
     -DHB_HAVE_FREETYPE=ON \
     -DHB_HAVE_GLIB=OFF \
     -DHB_HAVE_ICU=OFF \
diff --git a/scripts/deps/build-opencascade.sh b/scripts/deps/build-opencascade.sh
index fa6dec8..d35b78a 100755
--- a/scripts/deps/build-opencascade.sh
+++ b/scripts/deps/build-opencascade.sh
@@ -63,8 +63,8 @@ emcmake cmake "${OCC_DIR}" \
     -DCMAKE_POLICY_VERSION_MINIMUM=3.5 \
     -DCMAKE_BUILD_TYPE=${BUILD_TYPE:-Debug} \
     -DCMAKE_INSTALL_PREFIX="${SYSROOT}" \
-    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread" \
-    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread" \
+    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
+    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
     -DBUILD_LIBRARY_TYPE=Static \
     -DBUILD_MODULE_ApplicationFramework=OFF \
     -DBUILD_MODULE_Draw=OFF \
diff --git a/scripts/deps/build-pixman.sh b/scripts/deps/build-pixman.sh
index 06e9c60..e079525 100755
--- a/scripts/deps/build-pixman.sh
+++ b/scripts/deps/build-pixman.sh
@@ -77,7 +77,7 @@ cpu = 'wasm32'
 endian = 'little'
 
 [built-in options]
-c_args = [${MESON_DEBUG_FLAGS}, '-pthread']
+c_args = [${MESON_DEBUG_FLAGS}, '-pthread', '-matomics', '-mbulk-memory']
 c_link_args = ['-pthread']
 EOF
 
diff --git a/scripts/deps/build-protobuf.sh b/scripts/deps/build-protobuf.sh
index 85cf856..0094aa7 100755
--- a/scripts/deps/build-protobuf.sh
+++ b/scripts/deps/build-protobuf.sh
@@ -57,8 +57,8 @@ cd "${PROTOBUF_BUILD}"
 emcmake cmake "${PROTOBUF_DIR}" \
     -DCMAKE_BUILD_TYPE=${BUILD_TYPE:-Debug} \
     -DCMAKE_INSTALL_PREFIX="${SYSROOT}" \
-    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread" \
-    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread" \
+    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
+    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
     -Dprotobuf_BUILD_TESTS=OFF \
     -Dprotobuf_BUILD_EXAMPLES=OFF \
     -Dprotobuf_BUILD_PROTOC_BINARIES=OFF \
@@ -68,5 +68,16 @@ emcmake cmake "${PROTOBUF_DIR}" \
 emmake make -j${JOBS}
 emmake make install
 
+# Create symlinks without debug suffix for pkg-config compatibility
+# Protobuf CMake adds 'd' suffix for Debug builds but pkg-config expects 'libprotobuf'
+if [ -f "${SYSROOT}/lib/libprotobufd.a" ] && [ ! -f "${SYSROOT}/lib/libprotobuf.a" ]; then
+    ln -sf libprotobufd.a "${SYSROOT}/lib/libprotobuf.a"
+    log_info "Created libprotobuf.a symlink for pkg-config"
+fi
+if [ -f "${SYSROOT}/lib/libprotobuf-lited.a" ] && [ ! -f "${SYSROOT}/lib/libprotobuf-lite.a" ]; then
+    ln -sf libprotobuf-lited.a "${SYSROOT}/lib/libprotobuf-lite.a"
+    log_info "Created libprotobuf-lite.a symlink for pkg-config"
+fi
+
 create_stamp "${PROTOBUF_STAMP}"
 log_info "Protobuf build complete!"
diff --git a/scripts/deps/build-zstd.sh b/scripts/deps/build-zstd.sh
index 0c1d4f5..79b4fc9 100755
--- a/scripts/deps/build-zstd.sh
+++ b/scripts/deps/build-zstd.sh
@@ -62,8 +62,8 @@ emcmake cmake "${ZSTD_DIR}/build/cmake" \
     -DZSTD_BUILD_SHARED=OFF \
     -DZSTD_BUILD_STATIC=ON \
     -DZSTD_MULTITHREAD_SUPPORT=ON \
-    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread" \
-    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread"
+    -DCMAKE_C_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory" \
+    -DCMAKE_CXX_FLAGS="${DEBUG_CFLAGS:--g -O0} -pthread -matomics -mbulk-memory"
 
 emmake make -j${JOBS}
 emmake make install
diff --git a/scripts/kicad/build-pcbnew.sh b/scripts/kicad/build-pcbnew.sh
index b7fff72..e9083d0 100755
--- a/scripts/kicad/build-pcbnew.sh
+++ b/scripts/kicad/build-pcbnew.sh
@@ -87,9 +87,10 @@ else
 fi
 
 # Step 2: Build dependencies
+# Note: --with-occ for OpenCASCADE, but NOT ngspice since KICAD_SPICE=OFF
 if [ $SKIP_DEPS -eq 0 ]; then
     log_info "Building dependencies..."
-    "${SCRIPT_DIR}/../deps/build-all-deps.sh" --all
+    "${SCRIPT_DIR}/../deps/build-all-deps.sh" --with-occ
 else
     log_info "Skipping dependencies (--skip-deps specified)"
 fi
@@ -100,26 +101,33 @@ if [ $NO_CLEAN -eq 1 ] && check_stamp "${KICAD_STAMP}"; then
     exit 0
 fi
 
-# Step 4: Verify wxWidgets is built
+# Step 4: Build wxWidgets if not present
+WXWIDGETS_STAMP="${BUILD_ROOT}/stamps/wxwidgets.stamp"
 if [ ! -f "${WX_BUILD}/lib/libwx_baseu-3.2.a" ]; then
-    log_error "wxWidgets not found. Please build wxWidgets first with:"
-    log_error "  ./scripts/build-wxuniversal-wasm.sh"
-    exit 1
+    log_info "Building wxWidgets..."
+    "${SCRIPT_DIR}/../build-wxuniversal-wasm.sh" --no-clean
+    # Create stamp after successful build
+    touch "${WXWIDGETS_STAMP}"
+elif [ ! -f "${WXWIDGETS_STAMP}" ]; then
+    # Library exists but no stamp - create one
+    touch "${WXWIDGETS_STAMP}"
 fi
 
 log_info "Building KiCad PCBnew ${KICAD_VERSION} for WASM..."
 
 # Step 5: Set build type
 # Use environment DEBUG_BUILD if set, otherwise check local --debug flag
+# -fexceptions is required because wxWidgets is built with exceptions enabled
+# -matomics -mbulk-memory are required for shared memory (pthreads)
 if [ "${DEBUG_BUILD:-0}" = "1" ] || [ $DEBUG -eq 1 ]; then
     BUILD_TYPE="Debug"
-    EXTRA_FLAGS="-g -O0"
-    LINKER_DEBUG_FLAGS="-g -gsource-map"
+    EXTRA_FLAGS="-g -O0 -fexceptions -matomics -mbulk-memory"
+    LINKER_DEBUG_FLAGS="-g -gsource-map -fexceptions"
     log_info "Building KiCad in DEBUG mode (with source maps)"
 else
     BUILD_TYPE="Release"
-    EXTRA_FLAGS="-O2"
-    LINKER_DEBUG_FLAGS=""
+    EXTRA_FLAGS="-O2 -fexceptions -matomics -mbulk-memory"
+    LINKER_DEBUG_FLAGS="-fexceptions"
     log_info "Building KiCad in RELEASE mode"
 fi