Can Gradle jar multiple projects into one jar?

This should work for what you want to do. This should be in the root gradle build file.

subprojects.each { subproject -> evaluationDependsOn(subproject.path)}

task allJar(type: Jar, dependsOn: subprojects.assemble) {
   baseName = 'your-base-name'
   subprojects.each { subproject -> 
      from subproject.configurations.archives.allArtifacts.files.collect {
         zipTree(it)
       }
    }
 }

You can publish this by adding it as an archive:

artifacts {
   archives allJar
}

Here's my solution, which is a little bit simpler:

// Create a list of subprojects that you wish to include in the jar.  
def mainProjects = [':apps',':core',':gui',':io']
task oneJar( type: Jar , dependsOn: mainProjects.collect{ it+":compileJava"}) {
    baseName = 'name of jar'
    from files(mainProjects.collect{ project(it).sourceSets.main.output })
}

Code has been tested on Gradle 1.12