Docs, CI build and CLI interface improvements

[GDYendell]

Waiting on #301

This change aims to make it easier for new developers to get started using odin-data. There are a few unrelated parts:

• Docs with doxygen generated API
• Fixing / simplifying the dummy example so it is can be run easily and reliably
• Fix system tests that run in CI
• Tear out a lot of frameProcessor CLI options superceded by the json config

Note that this branch requires the changes in #301, so includes those commits for now.

The docs are still very much a work in progress, but this adds the foundation to start adding to them. The keys things are:

• There are a lot of warnings from the doxygen build about undocumented code
• There should be more prose-with-API docs for the most important things to know
  • I started with the obvious classes, but probably not everything and I haven't written much description on how to use them.
• Using the Python Tools is very out of date, but I have left because it is probably better to have it than not.
• Code Climate is not providing any coverage information - I notice we use codecov for odin-control, which might be better
• Diagrams to aid with descriptive parts
  • I would like to create some Excalidraw diagrams because they can be checked in to git and easily edited with a freely available web editor

[GDYendell]

@timcnicholls could you enable the docs build under Settings > Pages > Build and Deployment? Hopefully then it will run the build step. I am not sure if it will actually publish them until they are built on master.

[timcnicholls]

@timcnicholls could you enable the docs build under Settings > Pages > Build and Deployment? Hopefully then it will run the build step. I am not sure if it will actually publish them until they are built on master.

@GDYendell Sure. Which mode do you want? Deploy from branch or Github Actions?

[GDYendell]

I think just Deploy from branch and then gh-pages. It uses this action to deploy it.

[GDYendell]

Check for more docs content:

• https://github.com/stfc-aeg/odin-workshop
• https://github.com/odin-detector/odin-detector.github.io/tree/wip

[GDYendell]

This PR fixes a few existing issues. Check through and link them here.

[GDYendell]

Update references to SharedMemoryParser. Replaced with SharedMemoryManager in 9fc3b93c754ca2e24e274bd94bd9d3b889b1a2c4

[GDYendell]

Add note that setting N frames = 0 means run until explicit stop.

[GDYendell]

Check whether odin-data compiles with std=cxx11 compile flag

[GDYendell]

Superceded by #317, #318, #314