--- a/make/common/JdkNativeCompilation.gmk	Mon Jun 03 08:21:04 2019 -0700
+++ b/make/common/JdkNativeCompilation.gmk	Mon Jun 03 10:52:18 2019 -0700
@@ -122,7 +122,9 @@
   endif
 
   ifneq ($$($1_EXCLUDE_SRC_PATTERNS), )
-    $1_EXCLUDE_SRC := $$(call containing, $$($1_EXCLUDE_SRC_PATTERNS), $$($1_SRC))
+    $1_SRC_WITHOUT_WORKSPACE_ROOT := $$(patsubst $$(WORKSPACE_ROOT)/%, %, $$($1_SRC))
+    $1_EXCLUDE_SRC := $$(addprefix %, $$(call containing, $$($1_EXCLUDE_SRC_PATTERNS), \
+        $$($1_SRC_WITHOUT_WORKSPACE_ROOT)))
     $1_SRC := $$(filter-out $$($1_EXCLUDE_SRC), $$($1_SRC))
   endif