Problems with Maven repository indexing

I've recently updated my Clojure plugin to get repository information from Leiningen projects, and supply that to IntelliJ for indexing so that I can get autocompletions etc for Maven artifacts. My code is based on the Gradle integration. This works well for standard repos, but for any repo with a slightly different configuration, it doesn't work, e.g.:

• There's no way to supply authentication configuration for a repository
• There's no way to configure non-standard wagons (e.g. for repos hosted on S3)

I believe the Maven integration supports this, but in Maven-specific ways (i.e. reading settings.xml). What this means is that users using these sorts of repos get continuous popups on every project sync complaining that their repo isn't indexed. Additionally, there's no way to exclude a configured repo from the indexing process. I believe this problem also affects the Gradle plugin for the same reasons (https://youtrack.jetbrains.com/issue/IDEA-138029 was the most relevant I could find). 

Is there any way around this problem, or are there plans to fix it? I think for the moment I'll just have to not warn if any un-indexed repos have sync errors, but I really don't like masking errors by default.