Add the notion of SystemPipeline which isn't user facing

This is in preparation for the multi pipeline feature. It's helpful to have a separate class for internal pipelines that have slightly different behaviour characteristics from user created pipelines. Two examples:

* internal pipelines are never reloaded while user pipelines can be depending on the usage of `pipeline.reload.automatic`
* user facing pipelines can, when using stdin/generator/elasticsearch inputs, terminate logstash and users depend on this. A system pipeline will never terminate so it needs to be excluded from the logic used to decide when to quit