build.gradle

apply plugin: 'java'

group = 'com.acme'
version = '1.0'

dependencies {
  compile 'acme:a:1.0'
  compile 'acme:b:1.0'
}

repositories {
	mavenRepo urls: "file:///${toJavaPath(projectDir.absolutePath)}/lib"
}

private def toJavaPath(path) {
  return path.replace(File.separator, '/')
}

task jarWithDeps(type: Jar, dependsOn: classes) {
	archiveName = "${baseName}-by-gradle.${extension}"
	compileDeps = configurations.compile.collect { zipTree(it) }

	// this project's classes and all deps
	from sourceSets*.classesDir
	from compileDeps

  manifest {
  	attributes 'Main-Class': 'ReadSpi'
  }
}

task jarWithDeps2(type: Jar, dependsOn: classes) {
    mergeDir = "${buildDir}/merge"
    // might need a lazy var in a multi-module project where deps are inherited
    runtimeDeps = configurations.runtime.collect { zipTree(it) }
    myServiceConfig = 'META-INF/services/MyService.config'
    
    doFirst {
        new File(mergeDir).delete()
        mergeFiles(mergeDir, runtimeDeps, myServiceConfig)
    }
 
    // this project's classes and all deps
    from sourceSets*.classesDir
    from(runtimeDeps) {
        exclude myServiceConfig
    }
    from mergeDir
}
 
private def mergeFiles(targetDir, fileTrees, relativePath) {
  // prepare the merge
  mergedFile = new File("${targetDir}/${relativePath}")
  new File(mergedFile.parent).mkdirs()
 
  fileTrees*.matching({ include "**/${relativePath}" })*.each {
    mergedFile << it.bytes
  }
}