CodeQL fails to extract info of certain source files when compiling chromium v8

CodeQL CLI version: 2.16.4
OS: Ubuntu
Target Project: chromium [v8](https://chromium.googlesource.com/v8/v8.git), latest

Description:
When trying to create CodeQL database when compiling chromium V8, sometimes I see certain source files are missing from the result of extractor, which ended up with `Command-line error: language modes specified are incompatible`.

This is obvious when I tried building just some specific target object with ninja. For example, after doing the following
```
tools/dev/v8gen.py gen x64.debug
codeql database create -l cpp -c 'ninja -C out.gn/x64.debug/ obj/v8_initializers/builtins-collections-gen.o' --overwrite -- test
```
where `src/builtins/builtins-collections-gen.cc` is the major source of `obj/v8_initializers/builtins-collections-gen.o`, the cpp file does not show up in the resulting database src.zip. And if I do the following
```
tools/dev/v8gen.py gen x64.debug
ninja -C out.gn/x64.debug/ obj/v8_initializers/builtins-collections-gen.o
rm -f out.gn/x64.debug/obj/v8_initializers/builtins-collections-gen.o
codeql database create -l cpp -c 'ninja -C out.gn/x64.debug/ obj/v8_initializers/builtins-collections-gen.o' --overwrite -- test
```
Then the database creation will exit complaining no source code is seen.

After searching I found a similar issue #8755 where https://github.com/github/codeql/issues/8755#issuecomment-1101782379 commented to use extra config options. So I replace the call to `v8gen.py` with
```
tools/dev/v8gen.py x64.debug -- symbol_level=0 v8_symbol_level=0
```
Then everything works fine. I checked the very last compilation command of the target obj/v8_initializers/builtins-collections-gen.o, and it turns out like the following before and after the change:
```bash
#before
../../third_party/llvm-build/Release+Asserts/bin/clang++ -MMD -MF obj/v8_initializers/builtins-collections-gen.o.d -DUSE_UDEV -DUSE_AURA=1 -DUSE_GLIB=1 -DUSE_OZONE=1 -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_GNU_SOURCE -DCR_CLANG_REVISION=\"llvmorg-15-init-8609-g3254f468-1\" -DCOMPONENT_BUILD -D_LIBCPP_ABI_UNSTABLE -D_LIBCPP_ABI_VERSION=Cr -D_LIBCPP_ENABLE_NODISCARD -D_LIBCPP_DEBUG=0 -DCR_LIBCXX_REVISION=79a2e924d96e2fc1e4b937c42efd08898fa472d7 -DCR_SYSROOT_HASH=3c87f6561722292471f6d5e38df0e554f0f4f31c -D_DEBUG -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DCPPGC_VERIFY_HEAP -DENABLE_DISASSEMBLER -DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64 -DENABLE_GDB_JIT_INTERFACE -DOBJECT_PRINT -DVERIFY_HEAP -DV8_TRACE_MAPS -DV8_ENABLE_ALLOCATION_TIMEOUT -DV8_ENABLE_FORCE_SLOW_PATH -DV8_ENABLE_DOUBLE_CONST_STORE_CHECK -DV8_INTL_SUPPORT -DENABLE_HANDLE_ZAPPING -DV8_CODE_COMMENTS -DV8_ENABLE_DEBUG_CODE -DV8_ENABLE_HEAP_SNAPSHOT_VERIFY -DV8_SNAPSHOT_NATIVE_CODE_COUNTERS -DV8_USE_EXTERNAL_STARTUP_DATA -DV8_ATOMIC_OBJECT_FIELD_WRITES -DV8_ENABLE_LAZY_SOURCE_POSITIONS -DV8_SHARED_RO_HEAP -DV8_WIN64_UNWINDING_INFO -DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH -DV8_SHORT_BUILTIN_CALLS -DV8_EXTERNAL_CODE_SPACE -DV8_ENABLE_MAGLEV -DV8_ENABLE_WEBASSEMBLY -DV8_ALLOCATION_FOLDING -DV8_ALLOCATION_SITE_TRACKING -DV8_ADVANCED_BIGINT_ALGORITHMS -DV8_ENABLE_CHECKS -DV8_COMPRESS_POINTERS -DV8_COMPRESS_POINTERS_IN_SHARED_CAGE -DV8_31BIT_SMIS_ON_64BIT_ARCH -DV8_DEPRECATION_WARNINGS -DV8_IMMINENT_DEPRECATION_WARNINGS -DCPPGC_CAGED_HEAP -DV8_TARGET_ARCH_X64 -DV8_HAVE_TARGET_OS -DV8_TARGET_OS_LINUX -DDEBUG -DENABLE_SLOW_DCHECKS -DV8_RUNTIME_CALL_STATS -DBUILDING_V8_SHARED -DU_USING_ICU_NAMESPACE=0 -DU_ENABLE_DYLOAD=0 -DUSE_CHROMIUM_ICU=1 -DU_ENABLE_TRACING=1 -DU_ENABLE_RESOURCE_TRACING=0 -DICU_UTIL_DATA_IMPL=ICU_UTIL_DATA_FILE -DUSING_V8_BASE_SHARED -DUSING_V8_PLATFORM_SHARED -I../.. -Igen -I../../buildtools/third_party/libc++ -I../../include -Igen/include -I../../third_party/icu/source/common -I../../third_party/icu/source/i18n -Wall -Werror -Wextra -Wimplicit-fallthrough -Wunreachable-code-aggressive -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wloop-analysis -Wno-unneeded-internal-declaration -Wenum-compare-conditional -Wno-psabi -Wno-ignored-pragma-optimize -Wno-unqualified-std-cast-call -Wno-deprecated-non-prototype -Xclang -no-opaque-pointers -Wmax-tokens -Wshadow -fno-delete-null-pointer-checks -fno-ident -fno-strict-aliasing --param=ssp-buffer-size=4 -fstack-protector -funwind-tables -fPIC -pthread -fcolor-diagnostics -fmerge-all-constants -fcrash-diagnostics-dir=../../tools/clang/crashreports -mllvm -instcombine-lower-dbg-declare=0 -ffp-contract=off -fcomplete-member-pointers -m64 -msse3 -Wno-builtin-macro-redefined -D__DATE__= -D__TIME__= -D__TIMESTAMP__= -ffile-compilation-dir=. -no-canonical-prefixes -ftrivial-auto-var-init=pattern -fno-omit-frame-pointer -gdwarf-4 -g2 -gdwarf-aranges -gsplit-dwarf -ggnu-pubnames -Xclang -fuse-ctor-homing -Wheader-hygiene -Wstring-conversion -Wtautological-overlap-compare -Wmissing-field-initializers -Wno-shadow -Wunreachable-code -Wshorten-64-to-32 -O0 -fvisibility=default -Wexit-time-destructors -Wno-undefined-bool-conversion -Wno-tautological-undefined-compare -std=c++17 -Wno-trigraphs -fno-aligned-new -fno-exceptions -fno-rtti -nostdinc++ -isystem../../buildtools/third_party/libc++/trunk/include -isystem../../buildtools/third_party/libc++abi/trunk/include --sysroot=../../build/linux/debian_bullseye_amd64-sysroot -c ../../src/builtins/builtins-collections-gen.cc -o obj/v8_initializers/builtins-collections-gen.o

#after
../../third_party/llvm-build/Release+Asserts/bin/clang++ -MMD -MF obj/v8_initializers/builtins-collections-gen.o.d -DUSE_UDEV -DUSE_AURA=1 -DUSE_GLIB=1 -DUSE_OZONE=1 -D__STDC_CONSTANT_MACROS -D__STDC_FORMAT_MACROS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_GNU_SOURCE -DCR_CLANG_REVISION=\"llvmorg-15-init-7040-g50de659a-3\" -DCOMPONENT_BUILD -D_LIBCPP_ABI_UNSTABLE -D_LIBCPP_ABI_VERSION=Cr -D_LIBCPP_ENABLE_NODISCARD -D_LIBCPP_DEBUG=0 -DCR_LIBCXX_REVISION=79a2e924d96e2fc1e4b937c42efd08898fa472d7 -DCR_SYSROOT_HASH=60354520bb7001d8d0288a2ab82cec7efec9fa3d -D_DEBUG -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DCPPGC_VERIFY_HEAP -DENABLE_DISASSEMBLER -DV8_TYPED_ARRAY_MAX_SIZE_IN_HEAP=64 -DENABLE_GDB_JIT_INTERFACE -DOBJECT_PRINT -DVERIFY_HEAP -DV8_TRACE_MAPS -DV8_ENABLE_ALLOCATION_TIMEOUT -DV8_ENABLE_FORCE_SLOW_PATH -DV8_ENABLE_DOUBLE_CONST_STORE_CHECK -DV8_INTL_SUPPORT -DENABLE_HANDLE_ZAPPING -DV8_CODE_COMMENTS -DV8_ENABLE_DEBUG_CODE -DV8_ENABLE_HEAP_SNAPSHOT_VERIFY -DV8_SNAPSHOT_NATIVE_CODE_COUNTERS -DV8_USE_EXTERNAL_STARTUP_DATA -DV8_ATOMIC_OBJECT_FIELD_WRITES -DV8_ENABLE_LAZY_SOURCE_POSITIONS -DV8_SHARED_RO_HEAP -DV8_WIN64_UNWINDING_INFO -DV8_ENABLE_REGEXP_INTERPRETER_THREADED_DISPATCH -DV8_SHORT_BUILTIN_CALLS -DV8_EXTERNAL_CODE_SPACE -DV8_ENABLE_MAGLEV -DV8_ENABLE_WEBASSEMBLY -DV8_ALLOCATION_FOLDING -DV8_ALLOCATION_SITE_TRACKING -DV8_ADVANCED_BIGINT_ALGORITHMS -DV8_ENABLE_CHECKS -DV8_COMPRESS_POINTERS -DV8_COMPRESS_POINTERS_IN_SHARED_CAGE -DV8_31BIT_SMIS_ON_64BIT_ARCH -DV8_DEPRECATION_WARNINGS -DV8_IMMINENT_DEPRECATION_WARNINGS -DCPPGC_CAGED_HEAP -DV8_TARGET_ARCH_X64 -DV8_HAVE_TARGET_OS -DV8_TARGET_OS_LINUX -DDEBUG -DENABLE_SLOW_DCHECKS -DV8_RUNTIME_CALL_STATS -DBUILDING_V8_SHARED -DU_USING_ICU_NAMESPACE=0 -DU_ENABLE_DYLOAD=0 -DUSE_CHROMIUM_ICU=1 -DU_ENABLE_TRACING=1 -DU_ENABLE_RESOURCE_TRACING=0 -DICU_UTIL_DATA_IMPL=ICU_UTIL_DATA_FILE -DUSING_V8_BASE_SHARED -DUSING_V8_PLATFORM_SHARED -I../.. -Igen -I../../buildtools/third_party/libc++ -I../../include -Igen/include -I../../third_party/icu/source/common -I../../third_party/icu/source/i18n -Wall -Werror -Wextra -Wimplicit-fallthrough -Wunreachable-code-aggressive -Wthread-safety -Wno-missing-field-initializers -Wno-unused-parameter -Wloop-analysis -Wno-unneeded-internal-declaration -Wenum-compare-conditional -Wno-psabi -Wno-ignored-pragma-optimize -Wno-unqualified-std-cast-call -Wmax-tokens -Wshadow -fno-delete-null-pointer-checks -fno-ident -fno-strict-aliasing --param=ssp-buffer-size=4 -fstack-protector -funwind-tables -fPIC -pthread -fcolor-diagnostics -fmerge-all-constants -fcrash-diagnostics-dir=../../tools/clang/crashreports -mllvm -instcombine-lower-dbg-declare=0 -ffp-contract=off -fcomplete-member-pointers -m64 -msse3 -Wno-builtin-macro-redefined -D__DATE__= -D__TIME__= -D__TIMESTAMP__= -ffile-compilation-dir=. -no-canonical-prefixes -ftrivial-auto-var-init=pattern -fno-omit-frame-pointer -g0 -Wheader-hygiene -Wstring-conversion -Wtautological-overlap-compare -Wmissing-field-initializers -Wno-shadow -Wunreachable-code -Wshorten-64-to-32 -O0 -fvisibility=default -Wexit-time-destructors -Wno-undefined-bool-conversion -Wno-tautological-undefined-compare -std=c++17 -Wno-trigraphs -fno-aligned-new -fno-exceptions -fno-rtti -nostdinc++ -isystem../../buildtools/third_party/libc++/trunk/include -isystem../../buildtools/third_party/libc++abi/trunk/include --sysroot=../../build/linux/debian_bullseye_amd64-sysroot -c ../../src/builtins/builtins-collections-gen.cc -o obj/v8_initializers/builtins-collections-gen.o
```
It seems that the changed configuration removes the following clang options, which is key to the problem:
```
... -Wno-deprecated-non-prototype -Xclang -no-opaque-pointers ... -gdwarf-4 -g2 -gdwarf-aranges -gsplit-dwarf -ggnu-pubnames -Xclang -fuse-ctor-homing
```
Hopefully this helps.

The log of a failed database creation is attached below.
[build-tracer.log](https://github.com/github/codeql/files/14755012/build-tracer.log)