IntelliJ Gradle deletes its own modules unexpectedly - gradle

Question

This is the dialog indicating the modules which are being deleted
but when I import a new project with build.gradle and I do not enable auto import now I have a dialog asking my if I would like to enable auto import, and the modules are no longer deleted automatically.
Here is the build.gradle file
/*------------------------------------------------------------------------------
Gradle latest file.
Build command:
./gradlew deploy
Create Javadocs at ./latest/docs/javadoc/index.html
./gradlew buildJavadocs
Other commands of interest:
./gradlew wrapper --gradle-version 4.7
./gradlew tasks
./gradlew properties
Manual search for dependencies in Gradle repository:
https://bintray.com/bintray/jcenter/io.appium%3Ajava-client
------------------------------------------------------------------------------*/
group 'com.my.group'
version '1.0-SNAPSHOT'
apply plugin: 'java'
sourceSets {
main {
java {
srcDir 'src/'
}
}
}
sourceCompatibility = 1.8
repositories {
jcenter()
}
dependencies {
compile group: 'org.apache.commons', name: 'commons-lang3', version: '3.0'
compile 'junit:junit:4.12'
compile 'org.seleniumhq.selenium:selenium-java:3.11.0'
compile 'io.appium:java-client:6.1.0' // /compile 'io.appium:java-client:6.0.0-BETA5'
//compile 'io.appium:java-client:6.0.0-BETA5' // compile 'io.appium:java-client:6.1.0'
compile 'com.googlecode.json-simple:json-simple:1.1.1'
compile 'com.google.guava:guava:24.1-jre'
compile group: 'org.apache.commons', name: 'commons-io', version: '1.3.2'
}
task copyToLib(type: Copy, dependsOn: build) {
String dst = "$rootDir/jar"
description "Copy library JAR dependencies to $dst"
from configurations.runtime
into "$dst"
}
task copyToOut(type: Copy, dependsOn: build) {
String dst = "$rootDir/out"
description "Copy library JAR output to $dst"
from jar
into "$dst"
}
task deploy {
dependsOn clean
dependsOn build
dependsOn copyToLib
dependsOn copyToOut
}
task buildJavadocs(type: Javadoc) {
exclude 'srcOld/**'
classpath += sourceSets.test.compileClasspath
source += sourceSets.main.allJava
}
edit
When Gradle deletes the modules, it also delete gradle.build and the gradle wrapper. I've already created a brand new project with the default Java template, and copied and pasted my code into it, but the problem persists.

Answer 1

In case of a Gradle projects IDE configures the project structure including the modules that are included in project according your the build.gradle script. E.g. if you have Create separate module per source set option enabled in IDE Gradle settings IDE creates separate module for each Grale source set. It does it when re-importing build.gradle file. If you have auto-import enabled in IDE Gradle configuration it does it automatically.

Answer 2

Given the limited information, I'll give you an ad-hoc fix, just add -----test as a sub-project directory to your root projects settings.gradle using
include 'root-proj-dir:dir1:dir2:...:----test'
where the directory structure is
root-proj-dir
|
|
----dir1
| |
| |
| ----dir2
| |
| |
| ....----test
----settings.gradle
|
----build.gradle
For more info on dealing with multi-module (or multi-project in Gradle terminology ) builds refer this link