Would be ideal to get a review from @greg-1-anderson since he made #2982

Please see if #3495 (comment) fixes this for you.

This should be solved via configuration injection, as suggested in #3495 (comment).

If the issue is that only command-specific options are working here, and a global sites-subdir configuration option is not respected, we should investigate that and fix it in config injection. We don't want to add explicit calls to config->get() when it is possible to inject the value.

@greg-1-anderson that seems to be the case. Also, sites subdir resolution fails to fallback on default when a URI is provided. fix for that here #3591

I'm not sure how "If the issue is that only command-specific options are working here, and a global sites-subdir configuration option is not respected" should be addressed but I think the original issue has been addressed pretty thoroughly so closing this.