Made Pipelines user guide consistent and clearer

[jbednar]

Main changes:

• The first section was written as if there was only one output, but the code had two; looks like the markdown wasn't updated when the code was
• Removed stray , ready_parameter='ready', auto_advance=True in early example; looks like something meant for the last example
• Clarified hierarchical arrangement of .layout
• Cleaned up descriptions and narrative flow

I opened some issues found while reviewing this (#731, #732, #733, #734). When those are fixed, the text in this notebook will need to be updated accordingly, so this PR should probably be merged before addressing any of those (or updated each time).

One additional issue is that I wasn't sure why .init() needed to be called or precisely when it should be called; isn't there some way that it can be called automatically? It's a confusing, stateful thing...

[philippjfr]

The init issue can probably be solved thinking about it. The issue was that it wasn't obvious how to set up the graph when you declare a simple linear pipeline without calling define_graph, but if we simply build up the linear pipeline as stages are added and then override if define_graph is called there is no problem.

[jbednar]

That sounds right from what I remember of that code, thanks. I've opened #736 as a request to address that.

[philippjfr]

Changes look good thanks!