Q: How to create an Android Library Jar with gradle without publicly revealing source code? I would like to create a Jar out of an Android library project. It is set up the following way:
ProjectName
    \- lib
    |   \- lib
    |       \- armeabi
    |           \- libNativeFirst.so
    |           \- libNativeSecond.so
    \- src
        \- main
            \- java
                \- com.package.sdk
                    \- PackageSDK.java

I would like for all of this to be packaged in a Jar, but without revealing the source code present in PackageSDK.java.
I set up my build.gradle file like so:
buildscript {
    repositories {
        mavenCentral()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle:0.5.+'
    }
}

apply plugin: 'android-library'

repositories {
    mavenCentral()
}

android {
    compileSdkVersion 18
    buildToolsVersion "18.0.1"

    defaultConfig {
        minSdkVersion 10
        targetSdkVersion 18
    }

    sourceSets {
        main {
            java {
                srcDir 'src/main/java'
            }
            resources {
                srcDir 'src/../lib'
            }
        }
    }
}

task jar(type: Jar) {
    from android.sourceSets.main.allSource
}

When I run gradlew clean jar in the project's directory, a Jar file is created in ProjectName\build\libs called ProjectName.jar. It's structure is as follows:
ProjectName.jar
    \- lib
    |   \- armeabi
    |       \- libNativeFirst.so
    |       \- libNativeSecond.so
    \- com
        \- package
            \- sdk
                \- PackageSDK.java

I would like for the compiled PackageSDK.class to be included instead of the PackageSDK.java file when executing the jar task. What can I change to achieve this?
Edit:
Per Ben Manes's suggestion, I changed the configuration of the sourceSets to the following:
sourceSets {
    main {
        java {
            srcDir 'src/main/java'
        }
        resources {
            srcDir 'src/../lib'
        }
        output {
            classesDir 'build/classes'
            resourcesDir 'build/javaResources'
        }
    }
}

And the jar task to the following:
task jar(type: Jar) {
    from android.sourceSets.main.output
}

Gradle is now giving me this output:
Could not find method output() for arguments [build_25r1m0a3etn5cudtt5odlegprd$_run_closure2_closure9_closure10_closure13@138532dc] on source set main.

A: Just to add a slight alternative to @BVB's answer (although heavily based on it) here's what I had to do to output a jar myapp-api.jar which was for a Java only project that dealt with rest API interaction. It's dependant on Android.jar hence the need to use apply plugin: 'com.android.application' rather than just apply plugin: 'java' 
Calling ./gradlew build jar from the myJavaAPIProject to build and generate the .jar to   myJavaAPIProject/build/libs/myapp-api.jar 
build.gradle
//Even though this is a Java project, we need to apply the android plugin otherwise it cannot find the SDK/android.jar and so cannot compile
apply plugin: 'com.android.application'

dependencies {
    //this ensures we have gson.jar and anything else in the /lib folder
    compile fileTree(dir: 'lib', include: '*.jar')
}

repositories {
    mavenCentral()
}
android{
    compileSdkVersion 21
    buildToolsVersion "21.0.1"

    defaultConfig {
        minSdkVersion 10
        targetSdkVersion 21
    }

    sourceSets {
        main {
            java {
                //points to an empty manifest, needed just to get the build to work
                manifest.srcFile 'AndroidManifest.xml'
                //defined our src dir as it's not the default dir gradle looks for
                java.srcDirs = ['src']

            }
        }
    }

    //enforce java 7
    compileOptions {
        sourceCompatibility JavaVersion.VERSION_1_7
        targetCompatibility JavaVersion.VERSION_1_7
    }
}

//Actually created the .jar file
task jar(type: Jar) {
    //from android.sourceSets.main.java
    from 'build/intermediates/classes/release/'
    archiveName 'myapp-api.jar'
}

AndroidManifest.xml
<?xml version="1.0" encoding="utf-8"?>
<!-- this is a dummy file needed to ensure gradle validates and builds ok -->
<manifest
    package="com.myapp.android"
    />


A: Note: The answer has been edited. Please see the 07/28/2014 update below.
Here is a solution I ended up coming up with. There may be a better way available, but I have not found it yet.
android {
    compileSdkVersion 18
    buildToolsVersion "18.0.1"

    defaultConfig {
        minSdkVersion 10
        targetSdkVersion 18
    }

    sourceSets {
        main {
            java {
                srcDir 'src/main/java'
            }
            resources {
                srcDir 'src/../lib'
            }
        }
    }
}

task clearJar(type: Delete) {
    delete 'build/libs/ProjectName.jar'
}

task makeJar(type: Copy) {
    from('build/bundles/release/')
    into('build/libs/')
    include('classes.jar')
    rename ('classes.jar', 'ProjectName.jar')
}

makeJar.dependsOn(clearJar, build)

Running gradlew makeJar creates a ProjectName.jar in the build/libs directory. The structure of this jar is as follows:
ProjectName.jar
    \- lib
    |   \- armeabi
    |       \- libNativeFirst.so
    |       \- libNativeSecond.so
    \- com
        \- package
            \- sdk
                \- PackageSDK.class

This is the exact result I needed. I am now able to use ProjectName.jar successfully in other projects.
EDIT: While I am able to use the resulting jar in projects within Android Studio, I cannot do so in projects created in ADT due to a warning about native code being present inside a jar file. Supposedly there is a flag to turn off this check in settings, but it does not function correctly. Thus, if you want to create a library that uses native code, those using ADT will have to manually copy the armeabi directory into libs/.
07/28/2014 Update:
As of Android Studio 0.8.0, Gradle output directories have been changed and the configuration outlined above will not work. I have changed my configuration to the following:
task clearJar(type: Delete) {
    delete 'build/outputs/ProjectName.jar'
}

task makeJar(type: Copy) {
    from('build/intermediates/bundles/release/')
    into('build/outputs/')
    include('classes.jar')
    rename ('classes.jar', 'ProjectName.jar')
}

IMPORTANT: Please note that ProjectName.jar will now be placed into build/outputs/ and NOT into build/libs/.
