NEXUS-5993: Replace File.mkdirs with Files.createDirectories and other

Using new Java7 nio Files class to create directories.
This should help us better diagnose some IO relates problems, as Files unlike File does not hide IOEx.

Issue
https://issues.sonatype.org/browse/NEXUS-5993

CI
https://bamboo.zion.sonatype.com/browse/NX-OSSF17