gradle-intellij-plugin didn't pack the jar generated by proguard in the zip file.

You're not supposed to obfuscate the base Jar file but the instrumented one instead. Please rely on the output of the instrumentedJar task instead of jar.

Jakub Chrzanowski This is my proguard task:
 

tasks.register<proguard.gradle.ProGuardTask>("proguard") {
    verbose()

    configuration("proguard-rules.pro")

    injars(tasks.named("instrumentedJar")) // injars(tasks.named("jar"))

    outjars("build/${rootProject.name}-obfuscated.jar")

    val javaHome = System.getProperty("java.home")

    print("javaHome=$javaHome")
    if (properties("skipProguard").isPresent.not()) {
        File("$javaHome/jmods/")
            .listFiles()!!
            .forEach {
                libraryjars(it.absolutePath)
            }
    }

    libraryjars(configurations.compileClasspath.get())

    dontshrink()
    dontoptimize()
    adaptclassstrings("**.xml")
    adaptresourcefilecontents("**.xml") // or   adaptresourcefilecontents()
    overloadaggressively()
    printmapping("build/proguard-mapping.txt")

    target(JavaVersion.VERSION_17.toString())

    adaptresourcefilenames()
    optimizationpasses(9)
    allowaccessmodification()
    mergeinterfacesaggressively()
    renamesourcefileattribute("SourceFile")
    keepattributes("Exceptions,InnerClasses,Signature,Deprecated,SourceFile,LineNumberTable,*Annotation*,EnclosingMethod")
}

And the prepareSandbox:

prepareSandbox {
        if (properties("skipProguard").isPresent.not()) {
            dependsOn("proguard")
            doFirst {
                val original = File("build/libs/${rootProject.name}-${properties("pluginVersion")}.jar")
                println(original.absolutePath)
                val obfuscated = File("build/${rootProject.name}-obfuscated.jar")
                println(obfuscated.absolutePath)
                if (original.exists() && obfuscated.exists()) {
                    original.delete()
                    obfuscated.renameTo(original)
                    println("plugin file obfuscated")
                } else {
                    println("error: some file does not exist, plugin file not obfuscated")
                }
            }
        }
    }

But still, the chosen jar in the ZIP file is the normal one!