[SPARK-19664][SQL] put hive.metastore.warehouse.dir in hadoopconf to overwrite its original value

## What changes were proposed in this pull request?

In [SPARK-15959](https://issues.apache.org/jira/browse/SPARK-15959), we bring back the `hive.metastore.warehouse.dir` , while in the logic, when use the value of  `spark.sql.warehouse.dir` to overwrite `hive.metastore.warehouse.dir` , it set it to `sparkContext.conf` which does not overwrite the value is hadoopConf, I think it should put in `sparkContext.hadoopConfiguration` and overwrite the original value of hadoopConf

https://github.com/apache/spark/blob/master/sql/core/src/main/scala/org/apache/spark/sql/internal/SharedState.scala#L64

## How was this patch tested?
N/A

Author: windpiger <songjun@outlook.com>

Closes #16996 from windpiger/hivemetawarehouseConf.

sql/core/src/main/scala/org/apache/spark/sql/internal/SharedState.scala

@@ -42,9 +42,12 @@ private[sql] class SharedState(val sparkContext: SparkContext) extends Logging {
   val warehousePath: String = {
     val configFile = Utils.getContextOrSparkClassLoader.getResource("hive-site.xml")
     if (configFile != null) {
+      logInfo(s"loading hive config file: $configFile")
       sparkContext.hadoopConfiguration.addResource(configFile)
     }
 
+    // hive.metastore.warehouse.dir only stay in hadoopConf
+    sparkContext.conf.remove("hive.metastore.warehouse.dir")
     // Set the Hive metastore warehouse path to the one we use
     val hiveWarehouseDir = sparkContext.hadoopConfiguration.get("hive.metastore.warehouse.dir")
     if (hiveWarehouseDir != null && !sparkContext.conf.contains(WAREHOUSE_PATH.key)) {
@@ -61,10 +64,11 @@ private[sql] class SharedState(val sparkContext: SparkContext) extends Logging {
       // When neither spark.sql.warehouse.dir nor hive.metastore.warehouse.dir is set,
       // we will set hive.metastore.warehouse.dir to the default value of spark.sql.warehouse.dir.
       val sparkWarehouseDir = sparkContext.conf.get(WAREHOUSE_PATH)
-      sparkContext.conf.set("hive.metastore.warehouse.dir", sparkWarehouseDir)
+      logInfo(s"Setting hive.metastore.warehouse.dir ('$hiveWarehouseDir') to the value of " +
+        s"${WAREHOUSE_PATH.key} ('$sparkWarehouseDir').")
+      sparkContext.hadoopConfiguration.set("hive.metastore.warehouse.dir", sparkWarehouseDir)
       sparkWarehouseDir
     }
-
   }
   logInfo(s"Warehouse path is '$warehousePath'.")