IntelliJ Idea 16 CE gradle issues - intellij-idea

Question

In my gradle file I am trying to use the following to solve another issue. This is my gradle file:
group 'com.winapp'
version '1.0-SNAPSHOT'
apply plugin: 'java'
sourceCompatibility = 1.8
repositories {
mavenCentral()
}
dependencies {
compile fileTree(dir: 'src/main/java/libs', include: ['*.jar'])
compile 'com.intellij:forms_rt:6.0.5'
testCompile group: 'junit', name: 'junit', version: '4.11'
}
task copyDependenciesToTarget(type: Copy) {
println 'Copying dependencies to target...'
configurations.compile.collect().each { compileDependency ->
copy {
with from (compileDependency.getPath()) {
include '*'
}
into 'target/libs/libs'
}
}
}
build.dependsOn(copyDependenciesToTarget)
jar {
manifest.attributes(
"Main-Class": "Main",
"Class-Path": configurations.compile.collect { 'libs/' + it.getName()}.join(' ')
)
}
The problem are is this:
configurations.compile.collect().each { compileDependency ->
copy {
with from (compileDependency.getPath()) {
include '*'
}
into 'target/libs/libs'
}
}
When I run the application I get this Exception:
org.gradle.api.internal.file.copy.CopySpecWrapper_Decorated cannot be cast to org.gradle.api.internal.file.copy.CopySpecInternal
Main problem is, I have no idea how to fix this error, I simply want my project to create a JAR file that works with JDBC, using this gradle code seems to be a solution for that issue, but now I have run into another problem, yet again.
Please let me know if you require any additional information and thank you in advance. Literally, I cant even. This problem.
EDIT
As stated in the comments. My project runs fine when I run it through the IDE. There is an issue when I create a JAR file using gradle. The bare gradle file that IntelliJ created when I started the gradle project follows (Added the jar config so my Main class would be picked up):
group 'com.winapp'
version '1.0-SNAPSHOT'
apply plugin: 'java'
sourceCompatibility = 1.8
repositories {
mavenCentral()
}
dependencies {
compile fileTree(dir: 'src/main/java/libs', include: ['*.jar'])
compile 'com.intellij:forms_rt:6.0.5'
testCompile group: 'junit', name: 'junit', version: '4.11'
}
jar {
manifest.attributes(
"Main-Class": "Main",
"Class-Path": configurations.compile.collect { 'libs/' + it.getName()}.join(' ')
)
}
When I execute my app from terminal after the JAR has been created (keeping in mind there are no issues when hitting run in the IDE) with java -jar myAppName.jar:
java.lang.ClassNotFoundException: org.sqlite.JDBC
NOTE: Usually I get a full stack running a java app, but in this case the above is the only output.
I am using this JAR for my sqlite needs:
sqlite-jdbc-3.15.1
As a test I commented out the Sqlite usage in my application and the JAR file worked fine. My GUI was displayed and everything went as expected (all things considered). The JAR stops working when I add the sqlite JAR file usage (code). Added it the same as my other libs (like retrofit), so this seems to be quite a strange issue.
Please let me know if I have explained the issue correctly?