See combined output file out/combined_template.json sutible for flywheel's bids-curate.
It is built by removing any comments and combining all the rules within the template.
Importatnly, 00_template.json is named with leading 00 so it always sorted first. All other json files are expected to be rules.
The crux of the combination is this jq command.
jq -s '.[0] + {rules: .[1:]}' *.json
The Makefile documents the actual process.