re-structure Java API, add Scala API and consolidate the names of Java/Scala API

Makefile

@@ -84,7 +84,7 @@ $(DMLC_CORE)/libdmlc.a:
 $(RABIT)/lib/$(LIB_RABIT):
 	+ cd $(RABIT); make lib/$(LIB_RABIT); cd $(ROOTDIR)
 
-java: java/libxgboost4j.so
+jvm-packages: jvm-packages/lib/libxgboost4j.so
 
 SRC = $(wildcard src/*.cc src/*/*.cc)
 ALL_OBJ = $(patsubst src/%.cc, build/%.o, $(SRC)) $(PLUGIN_OBJS)
@@ -120,7 +120,8 @@ lib/libxgboost.dll lib/libxgboost.so: $(ALL_DEP)
 	@mkdir -p $(@D)
 	$(CXX) $(CFLAGS) -shared -o $@ $(filter %.o %a,  $^) $(LDFLAGS)
 
-java/libxgboost4j.so: java/xgboost4j_wrapper.cpp $(ALL_DEP)
+jvm-packages/lib/libxgboost4j.so: jvm-packages/xgboost4j/src/native/xgboost4j.cpp $(ALL_DEP)
+	@mkdir -p $(@D)
 	$(CXX) $(CFLAGS) $(JAVAINCFLAGS) -shared -o $@ $(filter %.cpp %.o %.a, $^) $(LDFLAGS)
 
 xgboost: $(CLI_OBJ) $(ALL_DEP)