[SPARK-13626][CORE] Avoid duplicate config deprecation warnings.

Three different things were needed to get rid of spurious warnings:
- silence deprecation warnings when cloning configuration
- change the way SparkHadoopUtil instantiates SparkConf to silence
  warnings
- avoid creating new SparkConf instances where it's not needed.

On top of that, I changed the way that Logging.scala detects the repl;
now it uses a method that is overridden in the repl's Main class, and
the hack in Utils.scala is not needed anymore. This makes the 2.11 repl
behave like the 2.10 one and set the default log level to WARN, which
is a lot better. Previously, this wasn't working because the 2.11 repl
triggers log initialization earlier than the 2.10 one.

I also removed and simplified some other code in the 2.11 repl's Main
to avoid replicating logic that already exists elsewhere in Spark.

Tested the 2.11 repl in local and yarn modes.

Author: Marcelo Vanzin <vanzin@cloudera.com>

Closes #11510 from vanzin/SPARK-13626.