If you want your new code to be fully integrated into the LabKey Server web interface, need to run as trusted code (instead of just invoking client APIs as a particular user), or need to access underlying data, features, or services that aren't exposed via a client API, you'll need to develop as an "real" LabKey module.

You can use many libraries, JDK 8 syntax (by tweaking the build.xml to allow it), etc in a LabKey module. You can't easily use libraries that assume that they're the main entry point into the application, such as Spring Boot and others.

While we only maintain IntelliJ configuration files, other external developers do use Eclipse, and you might find this information helpful:

https://www.labkey.org/announcements/home/Developer/Forum/thread.view?rowId=10435

That said, there's a lot that could be done using client APIs to integrate with LabKey Server from an external web application.

So, no clear answer, but hopefully some useful info anyway.

Thanks,
Josh