`System.out` is used for logging as opposed to slf4j

[JPercival]

Describe the bug Various parts of the tooling log errors / warnings to System.out instead of a logging framework. This makes it difficult to redirect logging to a file or to distinguish errors from the actual output. Here's an example:

IOUtils logging

This is prevalent throughout the tooling.

Ideally, all logging goes through a logging framework such that it can be redirected to a file or filtered according to the end-users' preference. Only output related to CLI operations should go directly to STDOUT.