Eradicate usage of FileUtils / File .chmod and move to the FileSystem abstraction

The built-in Ruby classes FileUtils.chmod and File.chmod do not behave correctly under Windows.

We do however have a nice method Puppet::Util::Windows::Security.set_mode(mode, path) that does it's best job to simulate a POSIX mode and roundtrip it properly.

All call sites that use the Ruby methods should be updated to use a new Puppet::FileSystem.chmod that delegates properly to the appropriate OS specific method.

This should be a fairly mechanical change to the codebase.