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How to create a JAR file from gradle that contains the .java fields (source code) as well

I am using gradle to build some a uber jar file, this jar file has dependencies and I used this guide to create the task that I can run
My task is like this btw I am using kotlin
tasks.register<Jar>("uberJar") {
archiveClassifier.set("uber")
from(sourceSets.main.get().output)
duplicatesStrategy = DuplicatesStrategy.EXCLUDE;
dependsOn(configurations.runtimeClasspath)
from({
configurations.runtimeClasspath.get().filter { it.name.endsWith("jar") }.map { zipTree(it) }
}})
What can I add to this task to add my .java files as well.
Also I don't really understand much of what is going on here like what actually is SourceSets?

Try adding this to your build.gradle.kts and see if it works:
tasks.named<ProcessResources>("processResources") {
from("src/main/java")
}
When your uber-JAR builds, it should contain the source files. Though this will also add the source files to any JAR. If that is not what you want, then you will need to configure something similar in the uber-JAR setup.

How to exclude source folder from jar file

How can I exclude a source folder from a jar file using Gradle Kotlin DSL?
The source sets are
sourceSets {
main {
java {
srcDirs("src/main/java")
srcDirs("src/util/java")
}
}
}
and I want to exclude src/util/java from Jars.
I tried
tasks {
withType<Jar> {
exclude("src/util/java/**")
}
}
but that does ot work because the string likely does not contain the source folder.
What is the best way to achieve this?

Try to filter in the compile task.
tasks.withType(JavaCompile) {
exclude '**/util/**/*.java'
}
but this is appropriate if you looking to exclude some specific files.
If the whole src folder (like util) is to be excluded, it would be better redefine the sourceSets.main.java to only src folders you need - for that module

Gradle copy command deprecated, breaks build

In Gradle 3.x I was able to get some xml mapping files to copy into the classes directory prior to build/jar via the following block:
copy{
from 'src/main/java/com/company/mapping'
into 'build/classes/main/java/com/company/mapping'
include '**/*.xml'
}
In Gradle 4.9 this has been deprecated in favor of:
task copyMappings(type: Copy){
from 'src/main/java/com/company/mapping'
into 'build/classes/main/java/com/company/mapping'
include '**/*.xml'
}
The copyMappings task succeeds, but build/jar does not wait for copyMappings to finish. I have tried variations on build.dependsOn and doFirst{ copyMappings } doLast{ build } but nothing seems to get me the desired effect of having the copied files in place in the 'into' path prior to jar.
This is for Windows 10.

This works for me with Gradle 4.9 on Mac OS:
apply plugin: 'java'
task copyMappings(type: Copy) {
from 'src/main/java/com/company/mapping'
into 'build/classes/main/java/com/company/mapping'
include '**/*.xml'
}
jar.dependsOn copyMappings
jar.doFirst {
assert new File("${projectDir}/build/classes/main/java/com/company/mapping/abc.xml").exists()
assert new File("${projectDir}/build/classes/main/java/com/company/mapping/def.xml").exists()
}
command line is gradle clean jar

I like to model things around source sets where appropriate as doing so let's the build work more reliably with a wide range of plugins and use cases. For example, imagine you want to run an application direct from its class files and resources rather than packaging it as a JAR first. You could make sure that the "run" task depends on the copy as well, but you'd have to do that for every instance where this is a requirement.
Source sets are the ideal solution because they have the concept of a runtime classpath, which will work for packaging, instrumentation, running, testing and so on.
With that in mind, I would go for this simple declaration and get rid of the copy task:
sourceSets {
main {
resources {
srcDir "src/main/java"
include "**/*.xml"
}
}
}
The XML files will end up in a different directory from your current approach, but that shouldn't matter unless you have tasks that assume the location rather than using the source set model to get the necessary information.
Note The above include directive applies to all the resources in src/main/resources as well. So if you have properties files or text files or anything else in there, they will be excluded. The simplest solution is to add all required resource file patterns to the include directive.

How do I specify an extra folder to be on the classpath for gradle's application plugin 'run' task?

I've successfully configured my gradle build script to create a zip distribution of my application with an extra 'config' folder at the root. This folder contains (at least right now) only one properties file in use by the application, and is on the classpath for the application.
What I'm looking for now, however, is a way to do the same with the 'run' task in the application plugin. When I try to run my application this way, (for testing), my program fails to run because of a class trying to access this properties file on the root of the classpath.
A bonus would be if I could get IntelliJ or Eclipse to also add this folder to its classpath just like the other folders (src/main/java, src/main/resources, ...) so I can run and debug my code from within the IDE without invoking a gradle task. I want to try to avoid as much as possible tying this code to any one IDE, so that when anybody needs to work on the project, they just need to import the build.gradle file and have the IDE make the appropriate config files it needs.
Here is my build.gradle file:
apply plugin: 'application'
mainClassName = "MainClass"
startScripts {
// Add config folder to classpath. Using workaround at
// https://discuss.gradle.org/t/classpath-in-application-plugin-is-building-always-relative-to-app-home-lib-directory/2012
classpath += files('src/dist/config')
doLast {
def windowsScriptFile = file getWindowsScript()
def unixScriptFile = file getUnixScript()
windowsScriptFile.text = windowsScriptFile.text.replace('%APP_HOME%\\lib\\config', '%APP_HOME%\\config')
unixScriptFile.text = unixScriptFile.text.replace('$APP_HOME/lib/config', '$APP_HOME/config')
}
}
repositories {
...
}
dependencies {
...
}
Likely what needs to happen is that I need to have the /src/dist/config folder to be copied into the build directory and added to the classpath, or have its contents be copied into a folder that is already on the classpath.

I ended up taking Opal's suggestion as a hint, and came up with the following solution. I added the following to my build.gradle file:
task processConfig(type: Copy) {
from('src/main/config') {
include '**/*'
}
into 'build/config/main'
}
classes {
classes.dependsOn processConfig
}
run {
classpath += files('build/config/main')
}
Alternatively, a simpler approach would be to add a runtime dependency to my project as such:
dependencies {
...
runtime files('src/main/config')
}
I didn't end up doing it this way, however, because my distribution package ended up having .properties files in the lib folder... and I'm just picky that way.

As you can see in the docs run is a task of type JavaExec. So classpath for it can be modified. Try to add config folder to the classpath. See here.

Changing your production source code location

According to the gradle user guide: http://www.gradle.org/docs/current/userguide/userguide.pdf top of page 41 "Gradle expects to find your production source code under src/main/java". How can I customize gradle to use with my current and different directory structure?

Take a look at the Gradle docs regarding source sets. You can specify your source directory like so:
sourceSets {
main {
java {
srcDir 'path/to/java/src'
}
}
}