Index: projects/CMakeLists.txt
===================================================================
--- projects/CMakeLists.txt
+++ projects/CMakeLists.txt
@@ -4,6 +4,14 @@
 file(GLOB entries *)
 foreach(entry ${entries})
   if(IS_DIRECTORY ${entry} AND EXISTS ${entry}/CMakeLists.txt)
+    # Do not allow tools like clang or clang-tools-extra in the projects directory
+    if(${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/clang)
+      message(FATAL_ERROR "clang must be placed under llvm/tools, not llvm/projects")
+    endif()
+    if((${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/extra) OR
+       (${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/clang-tools-extra))
+      message(FATAL_ERROR "clang-tools-extra (extra) must be placed under llvm/tools/clang/tools, not llvm/projects")
+    endif()
     if((NOT ${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/compiler-rt) AND
        (NOT ${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/dragonegg) AND
        (NOT ${entry} STREQUAL ${CMAKE_CURRENT_SOURCE_DIR}/libcxx) AND