Docs don't say which takes precedence: persistent cluster settings, or elasticsearch.yml

I would have thought elasticsearch.yml, but the exception in #3670 refers to a setting that I have in my .yml file anyway:

```
threadpool:
    search:
        type: fixed
        size: 24
        queue_size: -1
```

This suggests that ES is trying to parse and act on the persistent cluster setting, even though that's already been set in the .yml file.

Version: 0.90.3
