Index: CMakeLists.txt
===================================================================
--- CMakeLists.txt
+++ CMakeLists.txt
@@ -12,13 +12,33 @@
 mark_as_advanced(CMAKE_INSTALL_PREFIX)
 # On the other hand we often want to switch compiler or cflags
 mark_as_advanced(CLEAR CMAKE_C_COMPILER CMAKE_CXX_COMPILER CMAKE_LINKER
-  CMAKE_C_FLAGS CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_MINSIZEREL
+  CMAKE_C_FLAGS_DEBUG CMAKE_C_FLAGS_MINSIZEREL
   CMAKE_C_FLAGS_RELEASE CMAKE_C_FLAGS_RELWITHDEBINFO
-  CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_MINSIZEREL
+  CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_MINSIZEREL
   CMAKE_CXX_FLAGS_RELEASE CMAKE_CXX_FLAGS_RELWITHDEBINFO
-  CMAKE_EXE_LINKER_FLAGS CMAKE_EXE_LINKER_FLAGS_DEBUG
-  CMAKE_EXE_LINKER_FLAGS_MINSIZEREL CMAKE_EXE_LINKER_FLAGS_RELEASE
-  CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO)
+  CMAKE_EXE_LINKER_FLAGS_DEBUG CMAKE_EXE_LINKER_FLAGS_MINSIZEREL
+  CMAKE_EXE_LINKER_FLAGS_RELEASE CMAKE_EXE_LINKER_FLAGS_RELWITHDEBINFO)
+
+# Encourage people to use TEST_SUITE_C_FLAGS/TEST_SUITE_CXX_FLAGS so
+# CMAKE_C_FLAGS can be used exclusively by -C cachefiles for specifying
+# target flags without the user accidentally overriding them.
+set(EXPECTED_CMAKE_C_FLAGS "" CACHE STRING
+    "Allows cache files to disable the CMAKE_C_FLAGS warning message")
+mark_as_advanced(EXPECTED_CMAKE_C_FLAGS)
+if(NOT "${CMAKE_C_FLAGS}" STREQUAL "${EXPECTED_CMAKE_C_FLAGS}")
+  message(WARNING "
+Specifying CMAKE_C_FLAGS, CMAKE_CXX_FLAGS, \
+CMAKE_EXE_LINKER_FLAGS is discouraged. Use TEST_SUITE_C_FLAGS, \
+TEST_SUITE_CXX_FLAGS and TEST_SUITE_EXE_LINKER_FLAGS instead.\
+")
+endif()
+mark_as_advanced(CMAKE_C_FLAGS CMAKE_CXX_FLAGS CMAKE_EXE_LINKER_FLAGS)
+set(TEST_SUITE_C_FLAGS "" CACHE STRING "Flags used by the C compiler.")
+set(TEST_SUITE_CXX_FLAGS "${TEST_SUITE_C_FLAGS}" CACHE STRING "Flags used by the C++ compiler.")
+set(TEST_SUITE_EXE_LINKER_FLAGS "" CACHE STRING "Flags used by the linker.")
+set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${TEST_SUITE_C_FLAGS}")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${TEST_SUITE_CXX_FLAGS}")
+set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${TEST_SUITE_EXE_LINKER_FLAGS}")
 
 project(test-suite C CXX)
 
Index: cmake/caches/util/arch_flags.cmake
===================================================================
--- cmake/caches/util/arch_flags.cmake
+++ cmake/caches/util/arch_flags.cmake
@@ -2,3 +2,5 @@
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${ARCH_FLAGS}" CACHE STRING "")
 set(CMAKE_MODULE_LINKER_FLAGS "${CMAKE_MODULE_LINKER_FLAGS} ${ARCH_FLAGS}" CACHE STRING "")
 set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${ARCH_FLAGS}" CACHE STRING "")
+# Silence the warning in the toplevel CMakeLists.txt.
+set(EXPECTED_CMAKE_C_FLAGS "${CMAKE_C_FLAGS}" CACHE STRING "")