Update for windows to execute rake bootstrap and bin\logstash.bat

With the switch to minitar, the rake bootstrap command was broken in windows, accessing file in binary mode resolves the issue.
Also cleaned up the logstash.bat script to mimic more the logstash shell script (remove deps command and USE_RUBY envvar)
Also update jruby to security release 1.7.16.1


@electrical that's next on my list why jruby and kibana archive are untar each time I run rake bootstrap, so it's seems to be windows specific atm.