Add 'design reference' sec; detection flowchart

Add a new section to the manual, 'design reference', which can collect our understanding of how the pipeline is designed as we develop it (and will mean future developers don't have to undergo the same process!).

Also add a description of the current detection workflow, based on conversations on Fri 24 July. The section foreshadows the improvements to be made. Currently the description of the clustering and trigger control algorithms is marked as 'TBD' because we need more input to understand them.