diff --git a/.github/workflows/compile-check.yml b/.github/workflows/compile-check.yml
index 3dced860..f0f7ea0b 100644
--- a/.github/workflows/compile-check.yml
+++ b/.github/workflows/compile-check.yml
@@ -51,7 +51,7 @@ jobs:
         key: tools_libs
         path: |
           toolchain/bin
-          toolchain/include
+          toolchain/libcxx-include
           toolchain/cache-version-url.txt
     - name: Run setup
       run: tools/setup.py smo-main.nso
diff --git a/.github/workflows/test-compile.yml b/.github/workflows/test-compile.yml
index f23de386..7b5980dc 100644
--- a/.github/workflows/test-compile.yml
+++ b/.github/workflows/test-compile.yml
@@ -26,7 +26,7 @@ jobs:
         key: tools_libs
         path: |
           toolchain/bin
-          toolchain/include
+          toolchain/libcxx-include
           toolchain/cache-version-url.txt
     - name: Run simplified setup
       run: tools/setup.py --project
diff --git a/.gitignore b/.gitignore
index f6f07459..04159a26 100644
--- a/.gitignore
+++ b/.gitignore
@@ -50,6 +50,8 @@ perf.data.old
 
 # Tooling
 /toolchain/clang-*
+!/toolchain/clang-include
+toolchain/libcxx-include
 toolchain/include
 toolchain/cache-version-url.txt
 tools/check
diff --git a/toolchain/ToolchainNX64.cmake b/toolchain/ToolchainNX64.cmake
index c48c708f..4d9c9dec 100644
--- a/toolchain/ToolchainNX64.cmake
+++ b/toolchain/ToolchainNX64.cmake
@@ -47,6 +47,13 @@ add_compile_options(-fPIC)
 # Helps with matching as this causes Clang to emit debug type info even for dynamic classes
 # with undefined vtables.
 add_compile_options(-fstandalone-debug)
+# avoids reading system-wide headers on later clang versions (for example linter's libclang)
+add_compile_options(--gcc-toolchain=/nonexistant)
+# after all other includes, use fallback clang headers
+# => applied only when building this project normally, using system-wide (lib-)clang will use its own
+add_compile_options(-idirafter ${CMAKE_CURRENT_LIST_DIR}/clang-include)
+# custom libc++, provided in combination with clang-3.9.1
+include_directories(SYSTEM ${CMAKE_CURRENT_LIST_DIR}/libcxx-include)
 
 add_definitions(-D SWITCH)
 add_definitions(-D NNSDK)
@@ -56,5 +63,3 @@ add_link_options(-stdlib=libc++ -nostdlib)
 add_link_options(-fPIC -Wl,-Bsymbolic-functions -shared)
 # Use lld for performance reasons (and because we don't want a dependency on GNU tools)
 add_link_options(-fuse-ld=${ODYSSEY_CLANG_LLD})
-
-include_directories(SYSTEM ${CMAKE_CURRENT_LIST_DIR}/include)
diff --git a/lib/aarch64/arm_neon.h b/toolchain/clang-include/arm_neon.h
similarity index 100%
rename from lib/aarch64/arm_neon.h
rename to toolchain/clang-include/arm_neon.h
diff --git a/tools/setup.py b/tools/setup.py
index 328835b3..7adb0bcf 100755
--- a/tools/setup.py
+++ b/tools/setup.py
@@ -126,14 +126,18 @@ def setup_project_tools(tools_from_source):
         os.symlink(f"{get_repo_root()}/toolchain/bin/listsym", f"{get_repo_root()}/tools/listsym")
 
     with tempfile.TemporaryDirectory() as tmpdir:
-        if not exists_toolchain_file("include/__config"):
+        if exists_toolchain_file("include/__config"):  # old path to libcxx headers => moved to `libcxx-include`
+            print("Removing old libc++ headers...")
+            shutil.rmtree(f"{get_repo_root()}/toolchain/include")
+
+        if not exists_toolchain_file("libcxx-include/__config"):
             print(">>> Downloading llvm-3.9 libc++ headers...")
             path = tmpdir + "/libcxx-3.9.1.src.tar.xz"
             urllib.request.urlretrieve(LIBCXX_SRC_URL, path)
             print(">>> Extracting libc++ headers...")
             with tarfile.open(path) as f:
                 f.extractall(tmpdir, filter='tar')
-            shutil.copytree(f"{tmpdir}/libcxx-3.9.1.src/include", f"{get_repo_root()}/toolchain/include", dirs_exist_ok=True)
+            shutil.copytree(f"{tmpdir}/libcxx-3.9.1.src/include", f"{get_repo_root()}/toolchain/libcxx-include", dirs_exist_ok=True)
 
         if not exists_tool("check") or not exists_tool("decompme") or not exists_tool("listsym") or not exists_toolchain_file("bin/clang") or not exists_toolchain_file("bin/ld.lld"):