Add documentation for new ApPipeWithFakes

[BrunoSanchez]

This relates to changes made in DM-48896

[kfindeisen]

FTR, the DM-48896 changes are #223.

[kfindeisen]

While the Sphinx docs are impressive and helpful, what I actually asked for was a comment in <instrument>/ApPipeWithFakes.yaml saying that the cross-reference to _instruments/ApPipeWithFakes.yaml is to a generated file. That's where it actually needs to be documented to keep from being overlooked by someone looking through or editing the pipelines.

If you do keep the Sphinx docs, please make sure they're organized in a modular, topic-centric form that keeps each page focused and defers to related docs wherever possible. You may find DMTN-030 helpful if you're unfamiliar with this style. In particular, pipeline-with-fakes.rst is (re-?)documenting a lot of things that are really about the source injection framework, and it felt like it couldn't decide whether it's written for people running the pipeline or those working on ap_pipe itself.

Any time you are making documentation changes, especially to Sphinx, please build the documentation and proofread it. You can catch a lot of errors just by looking at the rendered HTML.

[kfindeisen]

Looks good!