Bug fixes for file input stream and checkpointing

- Fixed bugs in the file input stream that led the stream to fail due to transient HDFS errors (listing files when a background thread it deleting fails caused errors, etc.)
- Updated Spark's CheckpointRDD and Streaming's CheckpointWriter to use SparkContext.hadoopConfiguration, to allow checkpoints to be written to any HDFS compatible store requiring special configuration.
- Changed the API of SparkContext.setCheckpointDir() - eliminated the unnecessary 'useExisting' parameter. Now SparkContext will always create a unique subdirectory within the user specified checkpoint directory. This is to ensure that previous checkpoint files are not accidentally overwritten. 
- Fixed bug where setting checkpoint directory as a relative local path caused the checkpointing to fail.