Don't use special compiler flags.
Add upstream patch to make dependencies explicit; needed for ninja builds.
--- tools/CMakeLists.txt.orig	2014-03-15 15:11:32 UTC
+++ tools/CMakeLists.txt
@@ -4,7 +4,6 @@ PROJECT(${PROJECT})
 if(MSVC)
     set(CMAKE_CXX_FLAGS "/O3")
 else()
-    set(CMAKE_CXX_FLAGS "-O3 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64")
 endif()
 
 SET(CPP_SRC osmpbf-outline.cpp)
@@ -10,6 +10,8 @@ endif()
 SET(CPP_SRC osmpbf-outline.cpp)
 SET(HPP_SRC "")
 SET(C_SRC "")
+set_source_files_properties(${CPP_SRC}
+    OBJECT_DEPENDS "${CMAKE_SOURCE_DIR}/include/osmpbf/fileformat.pb.h;${CMAKE_SOURCE_DIR}/include/osmpbf/osmformat.pb.h")
 include_directories("${CMAKE_SOURCE_DIR}/include")
 
 add_executable(${PROJECT} ${HPP_SRC} ${CPP_SRC} ${C_SRC})