gem bundling refactor

- gem bundling now uses the standalone mechanism to generate a setup.rb file which add each individual gem into the load path. this considerably speeds up the logstash boot time. my tests shows it almost cut load time in half. 
- got rid of the custom Gemfile specs loading which did not work when trying to use a local unpublished gem.

after applying this you must:

```sh
rm vendor/jar/jruby-complete-*.jar
make vendor-jruby
rm -rf vendor/bundle/jruby
bin/logstash deps
```

@colinsurprenant strange indeed, on my side (Ubuntu 12.04) this got cleaned after bin/logstash deps