CodeQL default fails to setup java/kotlin scan, duplicate class

[slominskir]

Hi,
I've been using CodeQL on many repos, but switching it on for one particular repo fails with an error about a duplicate class found. No scanning appears to continue. Here is a screenshot:

Using IDEA IntelliJ to scan for duplicates and manually looking for duplicates has turned up nothing. The project builds and runs fine. Best I can figure is perhaps the Gradle Integration SourceSet, which references the Main SourceSet, is confusing CodeQL into thinking all source files in Main are duplicated in the Integration set. Here is the failing project:

https://github.com/JeffersonLab/jmyapi

Any tips on resolving this? Error indicates I should look into a log file for more details. Where can I find this log file?

Regards,

Ryan