XD-1989 Remove hadoop cmds' warning/deprecations

- Use appropriate argument `-R` for recursive `ls` command
to avoid deprecation message
- Set `org.apache.hadoop.util.NativeCodeLoader`'s logging level
to `ERROR` to avoid warning message while loading native hadoop library
- Remove `deprecated` method usage `org.apache.hadoop.fs.FileStatus.isDir()`
as we no longer support hadoop 1.x
should this say "Refer to" or possibly ", using `hadoop config fs`"?