Dependency issues with generated sources using Gradle and ANTLR

UPDATE (Fix):

I've fixed this by adding enough module dependencies in the project settings. This still gets overwritten by a gradle refresh but I don't think this will be a huge deal. However, if anyone knows how to make this fix stick in a robust manner, I'd love to know!

ORIGINAL:

I've tinkered quite a bit, but these tools are complex enough that I'm just gonna ask how they should fit together. I've created a minimal version of my error, which I'm posting on GitHub if that helps (I've included idea files as well).

I am using Gradle to pull in a dependency on ANTLR and running `gradle assemble` to build (this builds fine from command line). However, IntelliJ has a large number of "Cannot resolve symbol 'Parser'" type messages. First, here is my project structure:

Next, here is the generated ExpParser file which is generated from ANTLR:

Two things of note:

1. UsedByANTLR, imported on line 4, is in the normal gradle source set location. I have been able to get this to resolve, but only by updating files that get overridden by gradle when I refresh (to be accurate, I've gotten an identical problem to resolve in the full project I'm working on). I'd like a more permanent way to get this to work, but not the end of the world if there isn't one.
2. Parser belongs to `org.antlr.runtime` and should be imported on line 7. However, Intellij is indicating that this import statement is unused, and that Parser is unresolved. Further, when entering in `import org.antlr.runtime.` the only completion option is `*`, and I can't specify Parser by its fully qualified name `...extends org.antlr.runtime.Parser`.

How can I get things to play nicely with eachother?

EDIT: 

I'm using

• IntelliJ IDEA 2018.2.2 (Ultimate Edition)
  Build #IU-182.4129.33, built on August 21, 2018
  Licensed to Benjamin Kushigian
  Subscription is active until September 30, 2019
  For educational use only.
  JRE: 1.8.0_152-release-1248-b8 amd64
  JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
  Linux 4.4.0-142-generic

• ------------------------------------------------------------
  Gradle 4.8.1
  ------------------------------------------------------------
  
  Build time: 2018-06-21 07:53:06 UTC
  Revision: 0abdea078047b12df42e7750ccba34d69b516a22
  
  Groovy: 2.4.12
  Ant: Apache Ant(TM) version 1.9.11 compiled on March 23 2018
  JVM: 1.8.0_212 (Oracle Corporation 25.212-b03)
  OS: Linux 4.4.0-142-generic amd64
  
  

• Java 8
• Antlr 3.5.2