generated-projects | Sample projects generated by Celerio , a Jaxio

I'm not using IntelliJ on a regular basis but tried it in the context of this question and my impression is that gradle's idea plugin and IntelliJ's gradle plugin don't go well together. That is you should either use the idea gradle plugin and import as plain Java project or import as gradle project using IntelliJ's gradle plugin. Main reason is that the idea plugin and the IntelliJ plugin are generating slightly different iml-files (those files are holding the project dependencies - amongst others) which leads to lot of confusion when using both plugins together. As you specifically asked for the gradle idea plugin, I used this plugin and imported into IntelliJ as plain java project.

But to answer your question I found no evidence that the order of libraries on the classpath differs from the order as declared in the dependencies section of the gradle file, when using a flatDir repo. When using compile fileTree(dir: 'libs', include:['*.jar']) the order was actually broken as described in your question. That is, you should stick to using a flatDir repo.

I'm using gradle 4.9 and IntelliJ 2018.2.

This is my gradle file