Skip deletion of files in clearFiles().

This fixes an issue where Spark could delete
original files in the current working directory
that were added to the job using addFile().

There was also the potential for addFile() to
overwrite local files, which is addressed by
changing Utils.fetchFile() to log a warning
instead of overwriting a file with new contents.

This is a short-term fix; a better long-term
solution would be to remove the dependence on
storing files in the current working directory,
since we can't change the cwd from Java.
Add synchronization to LocalScheduler.updateDependencies().
Add addFile() and addJar() to JavaSparkContext.
Change Utils.fetchFile() warning to SparkException.
Merge pull request #345 from JoshRosen/fix/add-file

Fix deletion of files in current working directory by clearFiles()
Raise exception when hashing Java arrays (SPARK-597)
Mark key as not loading in CacheTracker even when compute() fails
Test with exception while computing cached RDD.
Remove some dead comments
Merge pull request #348 from JoshRosen/spark-597

Raise exception when hashing Java arrays (SPARK-597)
Merge pull request #349 from woggling/cache-finally

Avoid stalls when computation of cached RDD throws exception
Merge branch 'mesos' into dev-merge
Fixed compilation bug in RDDSuite created during merge for mesos/master.