diff --git a/Makefile b/Makefile
index 2d33363206..e3fd7d26f3 100644
--- a/Makefile
+++ b/Makefile
@@ -492,13 +492,25 @@ px4_sitl_default-clang:
 	@cd "$(SRC_DIR)"/build/px4_sitl_default-clang && cmake "$(SRC_DIR)" $(CMAKE_ARGS) -G"$(PX4_CMAKE_GENERATOR)" -DCONFIG=px4_sitl_default -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
 	@$(PX4_MAKE) -C "$(SRC_DIR)"/build/px4_sitl_default-clang
 
+# Paths to exclude from clang-tidy (auto-generated from .gitmodules + manual additions):
+# - All submodules (external code we consume, not edit)
+# - Test code (allowed looser style)
+# - Example code (educational, not production)
+# - Vendored third-party code (e.g., CMSIS_5)
+#
+# To add manual exclusions, append to CLANG_TIDY_EXCLUDE_EXTRA below.
+# Submodules are automatically excluded - no action needed when adding new ones.
+CLANG_TIDY_SUBMODULES := $(shell git config --file .gitmodules --get-regexp path | awk '{print $$2}' | tr '\n' '|' | sed 's/|$$//')
+CLANG_TIDY_EXCLUDE_EXTRA := src/systemcmds/tests|src/examples|src/modules/gyro_fft/CMSIS_5
+CLANG_TIDY_EXCLUDE := $(CLANG_TIDY_SUBMODULES)|$(CLANG_TIDY_EXCLUDE_EXTRA)
+
 clang-tidy: px4_sitl_default-clang
-	@cd "$(SRC_DIR)"/build/px4_sitl_default-clang && "$(SRC_DIR)"/Tools/run-clang-tidy.py -header-filter=".*\.hpp" -j$(j_clang_tidy) -p .
+	@cd "$(SRC_DIR)"/build/px4_sitl_default-clang && "$(SRC_DIR)"/Tools/run-clang-tidy.py -header-filter=".*\.hpp" -j$(j_clang_tidy) -exclude="$(CLANG_TIDY_EXCLUDE)" -p .
 
 # to automatically fix a single check at a time, eg modernize-redundant-void-arg
 #  % run-clang-tidy-4.0.py -fix -j4 -checks=-\*,modernize-redundant-void-arg -p .
 clang-tidy-fix: px4_sitl_default-clang
-	@cd "$(SRC_DIR)"/build/px4_sitl_default-clang && "$(SRC_DIR)"/Tools/run-clang-tidy.py -header-filter=".*\.hpp" -j$(j_clang_tidy) -fix -p .
+	@cd "$(SRC_DIR)"/build/px4_sitl_default-clang && "$(SRC_DIR)"/Tools/run-clang-tidy.py -header-filter=".*\.hpp" -j$(j_clang_tidy) -exclude="$(CLANG_TIDY_EXCLUDE)" -fix -p .
 
 # TODO: Fix cppcheck errors then try --enable=warning,performance,portability,style,unusedFunction or --enable=all
 cppcheck: px4_sitl_default
diff --git a/src/modules/gyro_fft/CMSIS_5/.clang-tidy b/src/modules/gyro_fft/CMSIS_5/.clang-tidy
deleted file mode 100644
index 64e1b8f404..0000000000
--- a/src/modules/gyro_fft/CMSIS_5/.clang-tidy
+++ /dev/null
@@ -1,120 +0,0 @@
----
-Checks:          '*,
-                  -android*,
-                  -bugprone-integer-division,
-                  -cert-dcl50-cpp,
-                  -cert-env33-c,
-                  -cert-err34-c,
-                  -cert-err58-cpp,
-                  -cert-msc30-c,
-                  -cert-msc50-cpp,
-                  -cert-flp30-c,
-                  -clang-analyzer-core.CallAndMessage,
-                  -clang-analyzer-core.NullDereference,
-                  -clang-analyzer-core.UndefinedBinaryOperatorResult,
-                  -clang-analyzer-core.uninitialized.Assign,
-                  -clang-analyzer-core.VLASize,
-                  -clang-analyzer-cplusplus.NewDelete,
-                  -clang-analyzer-cplusplus.NewDeleteLeaks,
-                  -clang-analyzer-deadcode.DeadStores,
-                  -clang-analyzer-optin.cplusplus.VirtualCall,
-                  -clang-analyzer-optin.performance.Padding,
-                  -clang-analyzer-security.FloatLoopCounter,
-                  -clang-analyzer-security.insecureAPI.strcpy,
-                  -clang-analyzer-unix.API,
-                  -clang-analyzer-unix.cstring.BadSizeArg,
-                  -clang-analyzer-unix.Malloc,
-                  -clang-analyzer-unix.MallocSizeof,
-                  -cppcoreguidelines-c-copy-assignment-signature,
-                  -cppcoreguidelines-interfaces-global-init,
-                  -cppcoreguidelines-no-malloc,
-                  -cppcoreguidelines-owning-memory,
-                  -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
-                  -cppcoreguidelines-pro-bounds-constant-array-index,
-                  -cppcoreguidelines-pro-bounds-pointer-arithmetic,
-                  -cppcoreguidelines-pro-type-const-cast,
-                  -cppcoreguidelines-pro-type-cstyle-cast,
-                  -cppcoreguidelines-pro-type-member-init,
-                  -cppcoreguidelines-pro-type-reinterpret-cast,
-                  -cppcoreguidelines-pro-type-union-access,
-                  -cppcoreguidelines-pro-type-vararg,
-                  -cppcoreguidelines-special-member-functions,
-                  -fuchsia-default-arguments,
-                  -fuchsia-overloaded-operator,
-                  -google-build-using-namespace,
-                  -google-explicit-constructor,
-                  -google-global-names-in-headers,
-                  -google-readability-braces-around-statements,
-                  -google-readability-casting,
-                  -google-readability-function-size,
-                  -google-readability-namespace-comments,
-                  -google-readability-todo,
-                  -google-runtime-int,
-                  -google-runtime-references,
-                  -hicpp-braces-around-statements,
-                  -hicpp-deprecated-headers,
-                  -hicpp-explicit-conversions,
-                  -hicpp-function-size,
-                  -hicpp-member-init,
-                  -hicpp-no-array-decay,
-                  -hicpp-no-assembler,
-                  -hicpp-no-malloc,
-                  -hicpp-signed-bitwise,
-                  -hicpp-special-member-functions,
-                  -hicpp-use-auto,
-                  -hicpp-use-equals-default,
-                  -hicpp-use-equals-delete,
-                  -hicpp-use-override,
-                  -hicpp-vararg,
-                  -llvm-header-guard,
-                  -llvm-include-order,
-                  -llvm-namespace-comment,
-                  -misc-incorrect-roundings,
-                  -misc-macro-parentheses,
-                  -misc-misplaced-widening-cast,
-                  -misc-redundant-expression,
-                  -misc-unconventional-assign-operator,
-                  -misc-unused-parameters,
-                  -modernize-deprecated-headers,
-                  -modernize-loop-convert,
-                  -modernize-pass-by-value,
-                  -modernize-return-braced-init-list,
-                  -modernize-use-auto,
-                  -modernize-use-bool-literals,
-                  -modernize-use-default-member-init,
-                  -modernize-use-emplace,
-                  -modernize-use-equals-default,
-                  -modernize-use-equals-delete,
-                  -modernize-use-override,
-                  -modernize-use-using,
-                  -performance-inefficient-string-concatenation,
-                  -performance-unnecessary-value-param,
-                  -readability-avoid-const-params-in-decls,
-                  -readability-braces-around-statements,
-                  -readability-container-size-empty,
-                  -readability-delete-null-pointer,
-                  -readability-else-after-return,
-                  -readability-function-size,
-                  -readability-implicit-bool-cast,
-                  -readability-implicit-bool-conversion,
-                  -readability-inconsistent-declaration-parameter-name,
-                  -readability-named-parameter,
-                  -readability-non-const-parameter,
-                  -readability-redundant-control-flow,
-                  -readability-redundant-declaration,
-                  -readability-redundant-member-init,
-                  -readability-simplify-boolean-expr,
-                  -readability-static-accessed-through-instance,
-                  -readability-static-definition-in-anonymous-namespace,
-                 '
-WarningsAsErrors: '*'
-CheckOptions:
-  - key:             google-readability-braces-around-statements.ShortStatementLines
-    value:           '1'
-  - key:             google-readability-function-size.BranchThreshold
-    value:           '600'
-  - key:             google-readability-function-size.LineThreshold
-    value:           '4000'
-  - key:             google-readability-function-size.StatementThreshold
-    value:           '4000'
-...
diff --git a/src/systemcmds/tests/.clang-tidy b/src/systemcmds/tests/.clang-tidy
deleted file mode 100644
index 9d2589717a..0000000000
--- a/src/systemcmds/tests/.clang-tidy
+++ /dev/null
@@ -1,119 +0,0 @@
----
-Checks:          '*,
-                  -android*,
-                  -bugprone-integer-division,
-                  -cert-dcl50-cpp,
-                  -cert-env33-c,
-                  -cert-err34-c,
-                  -cert-err58-cpp,
-                  -cert-msc30-c,
-                  -cert-msc50-cpp,
-                  -cert-flp30-c,
-                  -clang-analyzer-core.CallAndMessage,
-                  -clang-analyzer-core.NullDereference,
-                  -clang-analyzer-core.UndefinedBinaryOperatorResult,
-                  -clang-analyzer-core.uninitialized.Assign,
-                  -clang-analyzer-core.VLASize,
-                  -clang-analyzer-cplusplus.NewDelete,
-                  -clang-analyzer-cplusplus.NewDeleteLeaks,
-                  -clang-analyzer-deadcode.DeadStores,
-                  -clang-analyzer-optin.cplusplus.VirtualCall,
-                  -clang-analyzer-optin.performance.Padding,
-                  -clang-analyzer-security.FloatLoopCounter,
-                  -clang-analyzer-security.insecureAPI.strcpy,
-                  -clang-analyzer-unix.API,
-                  -clang-analyzer-unix.cstring.BadSizeArg,
-                  -clang-analyzer-unix.Malloc,
-                  -clang-analyzer-unix.MallocSizeof,
-                  -cppcoreguidelines-c-copy-assignment-signature,
-                  -cppcoreguidelines-interfaces-global-init,
-                  -cppcoreguidelines-no-malloc,
-                  -cppcoreguidelines-owning-memory,
-                  -cppcoreguidelines-pro-bounds-array-to-pointer-decay,
-                  -cppcoreguidelines-pro-bounds-constant-array-index,
-                  -cppcoreguidelines-pro-bounds-pointer-arithmetic,
-                  -cppcoreguidelines-pro-type-const-cast,
-                  -cppcoreguidelines-pro-type-cstyle-cast,
-                  -cppcoreguidelines-pro-type-member-init,
-                  -cppcoreguidelines-pro-type-reinterpret-cast,
-                  -cppcoreguidelines-pro-type-union-access,
-                  -cppcoreguidelines-pro-type-vararg,
-                  -cppcoreguidelines-special-member-functions,
-                  -fuchsia-default-arguments,
-                  -fuchsia-overloaded-operator,
-                  -google-build-using-namespace,
-                  -google-explicit-constructor,
-                  -google-global-names-in-headers,
-                  -google-readability-casting,
-                  -google-readability-function-size,
-                  -google-readability-namespace-comments,
-                  -google-readability-todo,
-                  -google-runtime-int,
-                  -google-runtime-references,
-                  -hicpp-braces-around-statements,
-                  -hicpp-deprecated-headers,
-                  -hicpp-explicit-conversions,
-                  -hicpp-function-size,
-                  -hicpp-member-init,
-                  -hicpp-no-array-decay,
-                  -hicpp-no-assembler,
-                  -hicpp-no-malloc,
-                  -hicpp-signed-bitwise,
-                  -hicpp-special-member-functions,
-                  -hicpp-use-auto,
-                  -hicpp-use-equals-default,
-                  -hicpp-use-equals-delete,
-                  -hicpp-use-override,
-                  -hicpp-vararg,
-                  -llvm-header-guard,
-                  -llvm-include-order,
-                  -llvm-namespace-comment,
-                  -misc-incorrect-roundings,
-                  -misc-macro-parentheses,
-                  -misc-misplaced-widening-cast,
-                  -misc-redundant-expression,
-                  -misc-unconventional-assign-operator,
-                  -misc-unused-parameters,
-                  -modernize-deprecated-headers,
-                  -modernize-loop-convert,
-                  -modernize-pass-by-value,
-                  -modernize-return-braced-init-list,
-                  -modernize-use-auto,
-                  -modernize-use-bool-literals,
-                  -modernize-use-default-member-init,
-                  -modernize-use-emplace,
-                  -modernize-use-equals-default,
-                  -modernize-use-equals-delete,
-                  -modernize-use-override,
-                  -modernize-use-using,
-                  -performance-inefficient-string-concatenation,
-                  -performance-unnecessary-value-param,
-                  -readability-avoid-const-params-in-decls,
-                  -readability-braces-around-statements,
-                  -readability-container-size-empty,
-                  -readability-delete-null-pointer,
-                  -readability-else-after-return,
-                  -readability-function-size,
-                  -readability-implicit-bool-cast,
-                  -readability-implicit-bool-conversion,
-                  -readability-inconsistent-declaration-parameter-name,
-                  -readability-named-parameter,
-                  -readability-non-const-parameter,
-                  -readability-redundant-control-flow,
-                  -readability-redundant-declaration,
-                  -readability-redundant-member-init,
-                  -readability-simplify-boolean-expr,
-                  -readability-static-accessed-through-instance,
-                  -readability-static-definition-in-anonymous-namespace,
-                 '
-WarningsAsErrors: '*'
-CheckOptions:
-  - key:             google-readability-braces-around-statements.ShortStatementLines
-    value:           '1'
-  - key:             google-readability-function-size.BranchThreshold
-    value:           '600'
-  - key:             google-readability-function-size.LineThreshold
-    value:           '4000'
-  - key:             google-readability-function-size.StatementThreshold
-    value:           '4000'
-...