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


our bootstrap command uses the vendor:all task so the jruby one should still be part of it.