In S3, retry the read from start after an unexpected EOF

S3 likes to reset busy connections (under the assumption that Amazon is under
a DDOS attack).  Wait 1/2sec, and then retry the read all over.
Also remove all googlish "readFully" calls to get better stack traces.
Also make sure all IOExceptions (in S3, HDFS & NFS persist layers) get reported
at least, even if they are otherwise ignored.