Merge pull request microsoft#55 from Microsoft/jywu/incr_fixup

fix for possible incremental build breaks.

cmake/external/mkldnn.cmake

@@ -11,6 +11,9 @@ set(MKLDNN_INCLUDE_DIR ${MKLDNN_INSTALL}/include)
 # patch for mkldnn_sgemm thread safety bug.
 # it can be removed once a fix is available in a validated mkldnn release version.
 set(MKLDNN_PATCH_COMMAND1 git apply ${CMAKE_SOURCE_DIR}/patches/mkldnn/mkldnn_sgemm.patch)
+set(MKLDNN_PATCH_COMMAND2 git apply ${CMAKE_SOURCE_DIR}/patches/mkldnn/platform.cmake.patch)
+# discard prior changes due to patching in mkldnn source to unblock incremental builds.
+set(MKLDNN_PATCH_DISCARD_COMMAND cd ${MKLDNN_SOURCE} && git checkout -- .)
 
 if(WIN32)
   set(MKLDNN_SHARED_LIB mkldnn.dll)
@@ -20,7 +23,6 @@ if(WIN32)
     set(MKLML_SHARED_LIB mklml.dll)
     set(IOMP5MD_SHARED_LIB libiomp5md.dll)
   endif()
-  set(MKLDNN_PATCH_COMMAND2 "")
 else()
   if (APPLE)
     set(MKLDNN_SHARED_LIB libmkldnn.0.dylib)
@@ -32,7 +34,6 @@ else()
     set(MKLML_SHARED_LIB libmklml_intel.so)
     set(IOMP5MD_SHARED_LIB libiomp5.so)
   endif()
-  set(MKLDNN_PATCH_COMMAND2 git apply ${CMAKE_SOURCE_DIR}/patches/mkldnn/platform.cmake.patch)
 endif()
 
 if(NOT onnxruntime_USE_MKLDNN OR EXISTS ${MKLDNN_SOURCE}/external)
@@ -43,7 +44,7 @@ ExternalProject_Add(project_mkldnn
     PREFIX mkl-dnn
     GIT_REPOSITORY ${MKLDNN_URL}
     GIT_TAG ${MKLDNN_TAG}
-    PATCH_COMMAND ${DOWNLOAD_MKLML} COMMAND ${MKLDNN_PATCH_COMMAND1} COMMAND ${MKLDNN_PATCH_COMMAND2}
+    PATCH_COMMAND ${DOWNLOAD_MKLML} COMMAND ${MKLDNN_PATCH_DISCARD_COMMAND} COMMAND ${MKLDNN_PATCH_COMMAND1} COMMAND ${MKLDNN_PATCH_COMMAND2}
     SOURCE_DIR ${MKLDNN_SOURCE}
     CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_INSTALL_PREFIX=${MKLDNN_INSTALL}
 )