[NEXUS-6015] Replace remaining Closeables.closeQuietly with commons-io IOUtils.closeQuitely

Signed-off-by: Alin Dreghiciu <adreghiciu@gmail.com>
[NEXUS-6015] Replace some more commons-io IOUtils.closeQuitely with try-with-resources

Signed-off-by: Alin Dreghiciu <adreghiciu@gmail.com>