Errors and warnings are printed to stderr.

Fixes https://github.com/aws/aws-cli/issues/820

cc @jamesls @danielgtaylor 
In the example I gave above, it _is_ the last file we try to sync.  Specifically I have three files in my directory, 1 that is unreadable.  Running the sync command I get:

```
# First sync, this output looks reasonable:

$ aws s3 sync . s3://bucket/syncme2/
warning: Skipping file /private/tmp/syncme/baz. File/Directory is not readable.
upload: ./foo to s3://bucket/syncme2/foo
upload: ./bar to s3://bucket/syncme2/bar
$

# Now running the same command again I get:

$ aws s3 sync . s3://bucket/syncme2/
warning: Skipping file /private/tmp/syncme/baz. File/Directory is not readable.
Completed 0 part(s) with ... file(s) remaining
$
```

The last line seems out of place to me and I don't think it should be there.  I'm not saying we shouldn't have progress messages, but it seems like there are cases where we print a progress message that shouldn't be printed, such as in my example above.

Given this behavior existed prior to this change (I only noticed because you're modifying this area of the code and it stood out), I would be ok with addressing this as a separate PR.