Why app/build/outputs/apk folder deleted during config phase

apply plugin: 'com.android.application'
apply plugin: 'android-apt'

import org.apache.tools.ant.filters.*;

def AAVersion = '3.2'

Date.metaClass.'static'.fromString = { str ->
    com.mdimension.jchronic.Chronic.parse(str).beginCalendar.time
}

project.ext {
    buildBranch = "NA"
    buildDate = new Date()
    buildGuid = "NA"
    buildNumber = 9999
    buildVersion = '1.0.0'
    debugAPKFileSpec = "NA"
    releaseAPKFileSpec = "NA"
}

def getBuildBranch() {
    if( System.getenv("BUILD_BRANCH") != null ) {
        project.buildBranch = System.getenv("BUILD_BRANCH");
    } else {
        def stdout = new ByteArrayOutputStream()
        exec{
            commandLine('git','rev-parse','--abbrev-ref','HEAD');
            standardOutput = stdout;
        }
        project.buildBranch = stdout.toString().trim();
    }
    return project.buildBranch;
}

def getBuildDate() {
    if( System.getenv("BUILD_DATE") != null ) {
        project.buildDate = Date.fromString(System.getenv("BUILD_DATE"));
    }
    return project.buildDate;
}

def getBuildGuid() {
    if( System.getenv("BUILD_GUID") != null ) {
        project.buildGuid = System.getenv("BUILD_GUID");
    } else {
        def stdout = new ByteArrayOutputStream()
        exec{
            commandLine("git", "rev-parse", "HEAD");
            standardOutput = stdout;
        }
        project.buildGuid = stdout.toString().trim().substring(0,11);
    }
    return project.buildGuid;
}

def getBuildKey() {
    if( System.getenv("BUILD_KEY") != null ) {
        project.buildGuid = System.getenv("BUILD_KEY");
    } else {
        project.buildGuid = InetAddress.getLocalHost().getHostName() + "-" + ((Date)getBuildDate()).time;
    }
    return project.buildGuid;
}

def getBuildNumber() {
    if( System.getenv("BUILD_NUMBER") != null ) {
        project.buildNumber = Integer.parseInt(System.getenv("BUILD_NUMBER"));
    }
    return project.buildNumber;
}

def getBuildVersion() {
    if( System.getenv("BUILD_VERSION") != null ) {
        project.buildVersion = System.getenv("BUILD_VERSION");
    }
    return project.buildVersion;
}

buildscript {
    repositories {
        mavenCentral()
        jcenter()
    }
    dependencies {
        classpath 'com.android.tools.build:gradle:1.5.0'
        classpath 'com.neenbedankt.gradle.plugins:android-apt:1.4'
        classpath 'org.codehaus.groovy.modules.http-builder:http-builder:0.5.2'

        // NOTE: Do not place your application dependencies here; they belong
        // in the individual module build.gradle files
    }
}

apt {
    arguments {
        resourcePackageName 'com.scout.ui'
        androidManifestFile variant.outputs[0].processResources.manifestFile
    }
}

android {
    compileSdkVersion 23
    buildToolsVersion "23.0.1"

    defaultConfig {
        applicationId "com.scout.scoutandroidapp"
        minSdkVersion 16
        testInstrumentationRunner "android.support.test.runner.AndroidJUnitRunner"
        targetSdkVersion 23
        versionCode getBuildNumber()
        versionName getBuildVersion()
    }

    signingConfigs {
        release {
            storeFile file("../keystore")
            storePassword "STOREPASS"
            keyAlias "KEYALIAS"
            keyPassword "KEYPASS"
        }
    }

    buildTypes {
        release {
            minifyEnabled false
            proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
            signingConfig signingConfigs.release
        }
        debug {
            debuggable true
        }
    }

    applicationVariants.all { variant ->
        variant.outputs.each { output ->
            delete output.outputFile.parent;
        }
    }

    applicationVariants.all { variant ->
        variant.outputs.each { output ->
            output.outputFile = new File(
                    output.outputFile.parent,
                    output.outputFile.name.replace(".apk", "-${variant.versionName}.${variant.versionCode}.apk").replace("app-", "scout-android-app-")
            )

            if(output.outputFile.name.toLowerCase().contains("-debug-")) {
                project.debugAPKFileSpec = output.outputFile.parent + "/" + output.outputFile.name;
            }
        }
    }
}

dependencies {
    compile fileTree(dir: 'libs', include: ['*.jar'])

    apt "org.androidannotations:androidannotations:$AAVersion"
    compile "org.androidannotations:androidannotations-api:$AAVersion"
    compile 'com.android.support:support-v4:23.1.1'
    compile 'com.android.support:appcompat-v7:23.1.1'
    compile 'com.android.support:recyclerview-v7:23.1.1'
    compile 'com.android.support:cardview-v7:23.1.1'
    compile 'com.android.support:design:23.1.1'
    compile 'com.squareup.retrofit:retrofit:1.9.0'
    compile files('libs/ormlite-android-4.48.jar')
    compile files('libs/ormlite-core-4.48.jar')
    compile 'com.nostra13.universalimageloader:universal-image-loader:1.9.4'
    compile 'de.greenrobot:eventbus:2.4.0'
    compile 'net.hockeyapp.android:HockeySDK:3.5.0'
    compile 'com.squareup.picasso:picasso:2.5.2'
    compile 'de.hdodenhof:circleimageview:2.0.0'
    compile('com.github.afollestad.material-dialogs:core:0.8.5.3@aar') {
        transitive = true
    }
    compile('com.mikepenz:materialdrawer:4.6.4@aar') {
        transitive = true
    }

    androidTestCompile ('com.android.support.test:runner:0.4.1') {
        exclude module: 'support-annotations'
    }

    androidTestCompile ('com.android.support.test.espresso:espresso-core:2.2.1') {
        exclude module: 'support-annotations'
    }
}

task deleteBuildInfo(type: Delete) {
    delete 'src/main/assets/build.json'
}

task deleteReleaseNotes(type: Delete) {
    delete 'HockeyAppDistributionReleaseNotes.txt'
}

task updateBuildInfo(type: Copy, dependsOn: deleteBuildInfo) {
    from '../build.json.sample'
    into 'src/main/assets'
    rename 'build.json.sample', 'build.json'
    filter(ReplaceTokens, tokens: [
            BUILD_BRANCH: getBuildBranch(),
            BUILD_DATE: getBuildDate().getDateTimeString(),
            BUILD_DIR: System.getenv('PWD'),
            BUILD_GUID: getBuildGuid(),
            BUILD_HOST: InetAddress.getLocalHost().getCanonicalHostName(),
            BUILD_KEY: getBuildKey(),
            BUILD_NUMBER: getBuildNumber().toString(),
            BUILD_USER: System.getenv('USER'),
            BUILD_VERSION: getBuildVersion()
    ])
}

task updateReleaseNotes(type: Copy, dependsOn: deleteReleaseNotes) {
    from '../HockeyAppDistributionReleaseNotes.md.sample'
    into '..'
    rename 'HockeyAppDistributionReleaseNotes.md.sample',
            'HockeyAppDistributionReleaseNotes.md'
    filter(ReplaceTokens, tokens: [
            BUILD_BRANCH: getBuildBranch(),
            BUILD_DATE: getBuildDate().getDateTimeString(),
            BUILD_DIR: System.getenv('PWD'),
            BUILD_GUID: getBuildGuid(),
            BUILD_HOST: InetAddress.getLocalHost().getCanonicalHostName(),
            BUILD_KEY: getBuildKey(),
            BUILD_NUMBER: getBuildNumber().toString(),
            BUILD_USER: System.getenv('USER'),
            BUILD_VERSION: getBuildVersion()
    ])
}

preBuild.dependsOn(['updateBuildInfo','updateReleaseNotes']);

task signJar << {
    def cmdLine = "jarsigner -storepass 'STOREPASS' -verbose -sigalg SHA1withRSA -digestalg SHA1 -keystore ~/.keystore " +
        "./app/build/outputs/apk/scout-android-app-release-unsigned-1.0.0." + getBuildNumber() + ".apk " +
        "-signedjar ./app/build/outputs/apk/scout-android-app-release-signed-1.0.0." + getBuildNumber() + ".apk KEYSTORE"
    println ("signJar cmdLine: " + cmdLine)
    exec {
        executable "sh"
        args "-c", cmdLine
    }
}

task alignJar << {
    def cmdLine = "zipalign -v 4 ./app/build/outputs/apk/scout-android-app-release-signed-1.0.0." + getBuildNumber() + ".apk " +
            "scout-android-app-release-signed-aligned-1.0.0." + getBuildNumber() + ".apk"
    println ("alignJar cmdLine: " + cmdLine)
    exec {
        executable "sh"
        args "-c", cmdLine
    }
}

task publishToHockeyApp {
    doLast {
        def puckCommandLine = "app_id='APIID' -api_token='APITOKEN' -submit='auto' -force='true' -download='true' -notify='true' -open='nothing' -notes_path='../HockeyAppDistributionReleaseNotes.md' -notes_type=markdown '$project.debugAPKFileSpec'";
        println("puckCommandLine: " + puckCommandLine);
        exec {
            executable "sh"
            args "-c", "/usr/local/bin/puck " + puckCommandLine
        }
    }
}

//alignJar.dependsOn(['signJar']);
//publishToHockeyApp.dependsOn(['alignJar']);

preBuild {
    doLast {
        println ("I am the prebuild task.");
    }
}

clean {
    doFirst {
        println ("I am the clean task. first");
    }
    println "I am clean task. middle"
    doLast {
        println ("I am the clean task. last");
    }
}

build {
    doLast {
        println ("I am the build tasks.");
    }
}