I do not think that is needed. The index directories are configured ad hoc via overrides to the configuration by Java properties, i.e. by passing -Dclouseau.dir=<path>. Please note that dev/run script still does that and it is Clouseau 3.x that ignores that. So instead of touching dev/run we should fix this regression in the Clouseau source code itself.

The index directories are configured ad hoc via overrides to the configuration by Java properties, i.e. by passing -Dclouseau.dir=

That is also a viable option. IMHO it's better to keep all configuration settings in one place (e.g. the clouseau.conf config file) for easier understanding. It's more difficult to follow if configuration is scattered across several files in the repo.

Also the CouchDB database files are located under dev/lib/node{n} - it makes sense to keep the Clouseau index files there as well.

I agree with gabor that the -Dclouseau.dir behaviour in clouseau should be restored.

See https://github.com/apache/couchdb/blob/main/dev/run#L888 where we already pass a per-instance value to clouseau, it's just clouseau 3.0 ignores it. I think configuration was changed from https://commons.apache.org/proper/commons-configuration/ to whatever zio ships with, and which was configured as follows;

// Load and monitor configuration file.
  val config = new CompositeConfiguration()
  config.addConfiguration(new SystemConfiguration())

  val fileName = if (args.length > 0) args(0) else "clouseau.ini"
  val reloadableConfig = new HierarchicalINIConfiguration(fileName)
  reloadableConfig.setReloadingStrategy(new FileChangedReloadingStrategy)
  config.addConfiguration(reloadableConfig)

namely, that it would read from a file but could be overridden by Java system properties.

The configuration is managed by the Typesafe Config library where Java properties mapping hence ad-hoc overrides are possible.