CLUSTER-4. Allow users to run port configuration utility at any time.

This commit modifies bento-cluster so that its port configuration utility
can be run by a user via the command `bento config`.  There are also
several changes for cleaner code / better looking output.

This commit also modifies bento-cluster so that "bento-managed" configuration
set via `bento config` is stored in XML files seperate from the main
Hadoop/HBase XML configuration files. The configuration utility now writes
empty Hadoop/HBase XML configuration files that include properties from the
bento-managed configuration files. This is done when the configuration files
are missing or when requested by the user via the flag --reset.

If bento-managed configuration resources exist, any port configuration
existing in those files will be used as the default values for ports by the
configuration utility. The flag --use-hadoop-defaults controls this behavior.

The utility will also prompt the user for port values, even if default ports
are open, when the flag --prompt is set.