To repro, just use the command below:

$ ninja -C out/Release -j1200 ../../chrome/browser/web_applications/components/web_app_shortcut_linux.cc^
ninja: Entering directory `out/Release'
[1/1] Regenerating ninja files
[11437/11437] CXX obj/chrome/browser/web_applications/components/components/web_app_shortcut_linux.o
FAILED: obj/chrome/browser/web_applications/components/components/web_app_shortcut_linux.o 
/usr/local/google/home/lfg/dev/goma/gomacc ../../third_party/llvm-build/Release+Asserts/bin/clang++ -MMD -MF obj/chrome/browser/web_applications/components/components/web_app_shortcut_linux.o.d -DV8_DEPRECATION_WARNINGS -DUSE_UDEV -DUSE_AURA=1 -DUSE_GLIB=1 -DUSE_NSS_CERTS=1 -DUSE_X11=1 -DFULL_SAFE_BROWSING -DSAFE_BROWSING_CSD -DSAFE_BROWSING_DB_LOCAL -DCHROMIUM_BUILD -DFIELDTRIAL_TESTING_ENABLED -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -DCR_CLANG_REVISION=\"338452-1\" -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -DCOMPONENT_BUILD -DCR_LIBCXX_REVISION=332543 -DCR_LIBCXXABI_REVISION=331450 -DCR_SYSROOT_HASH=4e7db513b0faeea8fb410f70c9909e8736f5c0ab -DNDEBUG -DNVALGRIND -DDYNAMIC_ANNOTATIONS_ENABLED=0 -DGLIB_VERSION_MAX_ALLOWED=GLIB_VERSION_2_32 -DGLIB_VERSION_MIN_REQUIRED=GLIB_VERSION_2_26 -DWEBP_EXTERN=extern -DGL_GLEXT_PROTOTYPES -DUSE_GLX -DUSE_EGL -DVK_NO_PROTOTYPES -DTOOLKIT_VIEWS=1 -DV8_USE_EXTERNAL_STARTUP_DATA -DGOOGLE_PROTOBUF_NO_RTTI -DGOOGLE_PROTOBUF_NO_STATIC_INITIALIZER -DHAVE_PTHREAD -DPROTOBUF_USE_DLLS -DBORINGSSL_SHARED_LIBRARY -DU_USING_ICU_NAMESPACE=0 -DU_ENABLE_DYLOAD=0 -DICU_UTIL_DATA_IMPL=ICU_UTIL_DATA_FILE -DUCHAR_TYPE=uint16_t -DWEBRTC_NON_STATIC_TRACE_EVENT_HANDLERS=0 -DWEBRTC_CHROMIUM_BUILD -DWEBRTC_POSIX -DWEBRTC_LINUX -DABSL_ALLOCATOR_NOTHROW=1 -DNO_MAIN_THREAD_WRAPPING -DSK_IGNORE_LINEONLY_AA_CONVEX_PATH_OPTS -DSK_HAS_PNG_LIBRARY -DSK_HAS_WEBP_LIBRARY -DSK_HAS_JPEG_LIBRARY -DSK_VULKAN_HEADER=\"../../skia/config/SkVulkanConfig.h\" -DSK_VULKAN=1 -DSKIA_DLL -DGR_GL_IGNORE_ES3_MSAA=0 -DSKCMS_API=__attribute__\(\(visibility\(\"default\"\)\)\) -DSK_SUPPORT_GPU=1 -DSK_GPU_WORKAROUNDS_HEADER=\"gpu/config/gpu_driver_bug_workaround_autogen.h\" -DVK_NO_PROTOTYPES -DLEVELDB_PLATFORM_CHROMIUM=1 -DUSING_V8_SHARED -DV8_DEPRECATION_WARNINGS -I../.. -Igen -I../../third_party/libwebp/src -I../../third_party/khronos -I../../gpu -I../../third_party/libyuv/include -I../../third_party/vulkan/include -I../../third_party/protobuf/src -Igen/protoc_out -I../../third_party/protobuf/src -I../../third_party/boringssl/src/include -I../../third_party/ced/src -I../../third_party/icu/source/common -I../../third_party/icu/source/i18n -I../../third_party/webrtc_overrides -I../../third_party/webrtc -I../../third_party/abseil-cpp -I../../skia/config -I../../skia/ext -I../../third_party/skia/include/c -I../../third_party/skia/include/config -I../../third_party/skia/include/core -I../../third_party/skia/include/effects -I../../third_party/skia/include/encode -I../../third_party/skia/include/gpu -I../../third_party/skia/include/images -I../../third_party/skia/include/lazy -I../../third_party/skia/include/pathops -I../../third_party/skia/include/pdf -I../../third_party/skia/include/pipe -I../../third_party/skia/include/ports -I../../third_party/skia/include/utils -I../../third_party/vulkan/include -I../../third_party/skia/third_party/vulkanmemoryallocator -I../../third_party/skia/src/gpu -I../../third_party/skia/src/sksl -I../../third_party/skia/modules/skottie/include -I../../third_party/vulkan/include -I../../third_party/leveldatabase -I../../third_party/leveldatabase/src -I../../third_party/leveldatabase/src/include -I../../third_party/libwebm/source -I../../v8/include -Igen/v8/include -I../../third_party/perfetto/include -Igen/third_party/perfetto/protos -Igen/third_party/perfetto/protos -Igen/third_party/perfetto/protos -fno-strict-aliasing --param=ssp-buffer-size=4 -fstack-protector -Wno-builtin-macro-redefined -D__DATE__= -D__TIME__= -D__TIMESTAMP__= -funwind-tables -fPIC -B../../third_party/binutils/Linux_x64/Release/bin -pthread -fcolor-diagnostics -fmerge-all-constants -Xclang -mllvm -Xclang -instcombine-lower-dbg-declare=0 -no-canonical-prefixes -fcomplete-member-pointers -m64 -march=x86-64 -Wall -Werror -Wextra -Wimplicit-fallthrough -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wno-c++11-narrowing -Wno-covered-switch-default -Wno-unneeded-internal-declaration -Wno-undefined-var-template -Wno-nonportable-include-path -Wno-user-defined-warnings -Wno-unused-lambda-capture -Wno-null-pointer-arithmetic -Wno-enum-compare-switch -Wno-ignored-pragma-optimize -O2 -fno-ident -fdata-sections -ffunction-sections -fno-omit-frame-pointer -g0 -fvisibility=hidden -Xclang -load -Xclang ../../third_party/llvm-build/Release+Asserts/lib/libFindBadConstructs.so -Xclang -add-plugin -Xclang find-bad-constructs -Xclang -plugin-arg-find-bad-constructs -Xclang enforce-in-thirdparty-webkit -Xclang -plugin-arg-find-bad-constructs -Xclang check-enum-max-value -Xclang -plugin-arg-find-bad-constructs -Xclang check-ipc -Wheader-hygiene -Wstring-conversion -Wtautological-overlap-compare -isystem../../build/linux/debian_sid_amd64-sysroot/usr/include/glib-2.0 -isystem../../build/linux/debian_sid_amd64-sysroot/usr/lib/x86_64-linux-gnu/glib-2.0/include -Wexit-time-destructors -Wno-header-guard -isystem../../build/linux/debian_sid_amd64-sysroot/usr/include/nss -isystem../../build/linux/debian_sid_amd64-sysroot/usr/include/nspr -std=gnu++14 -fno-exceptions -fno-rtti -nostdinc++ -isystem../../buildtools/third_party/libc++/trunk/include -isystem../../buildtools/third_party/libc++abi/trunk/include --sysroot=../../build/linux/debian_sid_amd64-sysroot -fvisibility-inlines-hidden -c ../../chrome/browser/web_applications/components/web_app_shortcut_linux.cc -o obj/chrome/browser/web_applications/components/components/web_app_shortcut_linux.o
In file included from ../../chrome/browser/web_applications/components/web_app_shortcut_linux.cc:22:
../../chrome/browser/shell_integration_linux.h:11:10: fatal error: 'chrome/common/buildflags.h' file not found
#include "chrome/common/buildflags.h"
         ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
ninja: build stopped: subcommand failed.

loyso@, I'm assigning to you since you were the last person to change that file, can you take a look or reassign?