/usr/lib/llvm-3.9/include/clang/Tooling/ is in libclang-3.9-dev 1:3.9.1-19ubuntu1.
This file is owned by root:root, with mode 0o755.
..
/usr/lib/llvm-3.9/include/clang/Tooling/ArgumentsAdjusters.h
/usr/lib/llvm-3.9/include/clang/Tooling/CommonOptionsParser.h
/usr/lib/llvm-3.9/include/clang/Tooling/CompilationDatabase.h
/usr/lib/llvm-3.9/include/clang/Tooling/CompilationDatabasePluginRegistry.h
/usr/lib/llvm-3.9/include/clang/Tooling/Core/
/usr/lib/llvm-3.9/include/clang/Tooling/Core/Lookup.h
/usr/lib/llvm-3.9/include/clang/Tooling/Core/QualTypeNames.h
/usr/lib/llvm-3.9/include/clang/Tooling/Core/Replacement.h
/usr/lib/llvm-3.9/include/clang/Tooling/FileMatchTrie.h
/usr/lib/llvm-3.9/include/clang/Tooling/FixIt.h
/usr/lib/llvm-3.9/include/clang/Tooling/JSONCompilationDatabase.h
/usr/lib/llvm-3.9/include/clang/Tooling/Refactoring.h
/usr/lib/llvm-3.9/include/clang/Tooling/RefactoringCallbacks.h
/usr/lib/llvm-3.9/include/clang/Tooling/ReplacementsYaml.h
/usr/lib/llvm-3.9/include/clang/Tooling/Tooling.h