Refactor and document collection operations #3751

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Run time

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Job	Run time
Benchmark	1m 40s
Encoders	4m 53s
FHIR server (tranche 1)	1m 39s
Docker image	1m 26s
FHIR server (tranche 2)	1m 22s
FHIR server (tranche 3)	3s
JavaScript client	44s
Import lambda	54s
Python API	1m 28s
R API	4m 14s
Site	4m 45s
Pre-release deployment	0s
Upload coverage	0s
	23m 8s