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I went on to do some tests and found two options to add them in from the Endeca side.
1 - Add an override file.
Create the api_input directory in your config directory. Create a file called precedence_rules.csv and add your rules in there. This is documented in page 12 of
2 - Inject a precedence rule into the <app_name>enprules record store
The discover-data-cas project ships with a script called index_config_cmd.sh. Copy it and the necessary jar files to your project and you can insert a JSON file containing your rules with the following command.
./index_config_cmd.sh set-config -f precedence_rule_test.json
You can check the current set with the following command
./index_config_cmd.sh get-config -t precedenceRules
I was worried that these may be clobbered next time I ran a baseline update from the ProductCatalogSimpleIndexingAdmin module but it was not.
This option is documented in Chapter 4 of