[SPARK-16540][YARN][CORE] Avoid adding jars twice for Spark running on yarn

## What changes were proposed in this pull request?

Currently when running spark on yarn, jars specified with --jars, --packages will be added twice, one is Spark's own file server, another is yarn's distributed cache, this can be seen from log:
for example:

```
./bin/spark-shell --master yarn-client --jars examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar
```

If specified the jar to be added is scopt jar, it will added twice:

```
...
16/07/14 15:06:48 INFO Server: Started 5603ms
16/07/14 15:06:48 INFO Utils: Successfully started service 'SparkUI' on port 4040.
16/07/14 15:06:48 INFO SparkUI: Bound SparkUI to 0.0.0.0, and started at http://192.168.0.102:4040
16/07/14 15:06:48 INFO SparkContext: Added JAR file:/Users/sshao/projects/apache-spark/examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar at spark://192.168.0.102:63996/jars/scopt_2.11-3.3.0.jar with timestamp 1468480008637
16/07/14 15:06:49 INFO RMProxy: Connecting to ResourceManager at /0.0.0.0:8032
16/07/14 15:06:49 INFO Client: Requesting a new application from cluster with 1 NodeManagers
16/07/14 15:06:49 INFO Client: Verifying our application has not requested more than the maximum memory capability of the cluster (8192 MB per container)
16/07/14 15:06:49 INFO Client: Will allocate AM container, with 896 MB memory including 384 MB overhead
16/07/14 15:06:49 INFO Client: Setting up container launch context for our AM
16/07/14 15:06:49 INFO Client: Setting up the launch environment for our AM container
16/07/14 15:06:49 INFO Client: Preparing resources for our AM container
16/07/14 15:06:49 WARN Client: Neither spark.yarn.jars nor spark.yarn.archive is set, falling back to uploading libraries under SPARK_HOME.
16/07/14 15:06:50 INFO Client: Uploading resource file:/private/var/folders/tb/8pw1511s2q78mj7plnq8p9g40000gn/T/spark-a446300b-84bf-43ff-bfb1-3adfb0571a42/__spark_libs__6486179704064718817.zip -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/__spark_libs__6486179704064718817.zip
16/07/14 15:06:51 INFO Client: Uploading resource file:/Users/sshao/projects/apache-spark/examples/target/scala-2.11/jars/scopt_2.11-3.3.0.jar -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/scopt_2.11-3.3.0.jar
16/07/14 15:06:51 INFO Client: Uploading resource file:/private/var/folders/tb/8pw1511s2q78mj7plnq8p9g40000gn/T/spark-a446300b-84bf-43ff-bfb1-3adfb0571a42/__spark_conf__326416236462420861.zip -> hdfs://localhost:8020/user/sshao/.sparkStaging/application_1468468348998_0009/__spark_conf__.zip
...
```

So here try to avoid adding jars to Spark's fileserver unnecessarily.

## How was this patch tested?

Manually verified both in yarn client and cluster mode, also in standalone mode.

Author: jerryshao <[email protected]>

Closes #14196 from jerryshao/SPARK-16540.

Author: jerryshao

core/src/main/scala/org/apache/spark/util/Utils.scala

@@ -2409,9 +2409,9 @@ private[spark] object Utils extends Logging {
    * "spark.yarn.dist.jars" properties, while in other modes it returns the jar files pointed by
    * only the "spark.jars" property.
    */
-  def getUserJars(conf: SparkConf): Seq[String] = {
+  def getUserJars(conf: SparkConf, isShell: Boolean = false): Seq[String] = {
     val sparkJars = conf.getOption("spark.jars")
-    if (conf.get("spark.master") == "yarn") {
+    if (conf.get("spark.master") == "yarn" && isShell) {
       val yarnJars = conf.getOption("spark.yarn.dist.jars")
       unionFileLists(sparkJars, yarnJars).toSeq
     } else {

repl/scala-2.10/src/main/scala/org/apache/spark/repl/SparkILoop.scala

@@ -1066,7 +1066,7 @@ class SparkILoop(
       logWarning("ADD_JARS environment variable is deprecated, use --jar spark submit argument instead")
     }
     val jars = {
-      val userJars = Utils.getUserJars(conf)
+      val userJars = Utils.getUserJars(conf, isShell = true)
       if (userJars.isEmpty) {
         envJars.getOrElse("")
       } else {

repl/scala-2.11/src/main/scala/org/apache/spark/repl/Main.scala

@@ -54,7 +54,7 @@ object Main extends Logging {
   // Visible for testing
   private[repl] def doMain(args: Array[String], _interp: SparkILoop): Unit = {
     interp = _interp
-    val jars = Utils.getUserJars(conf).mkString(File.pathSeparator)
+    val jars = Utils.getUserJars(conf, isShell = true).mkString(File.pathSeparator)
     val interpArguments = List(
       "-Yrepl-class-based",
       "-Yrepl-outdir", s"${outputDir.getAbsolutePath}",