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- got rid of the custom Gemfile specs loading which did not work when trying to use a local unpublished gem.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
make vendor-jruby
bin/logstash deps
```

probably, we have to sync for the plugins and see the impact. this does not prevent setting the GEM_PATH and GEM_HOME but there are not necessary in the current context using the setup.rb with add all individual gems in the load path.