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it is possible to update Cordova plugins 3.6.0 to 6.2.0 manually (without CLI)?

I have an android project created with cordova 3.6.0, but cordova 6.2.0 CLI doesn't recognize it. I've tried to update cordova plugin manually firstly by replacing .java and .js plugin files but doesn't work, my app doesn't find the .js files, then I've tried to creating new cordova project with command cordova create and import all the class from my previous project but android Studio doesn't compile it for this reason :

com.android.build.api.transform.TransformException: java.util.zip.ZipException: duplicate entry: org/apache/cordova/AuthenticationToken.class

this is my build.gradle

/*
       Licensed to the Apache Software Foundation (ASF) under one
       or more contributor license agreements.  See the NOTICE file
       distributed with this work for additional information
       regarding copyright ownership.  The ASF licenses this file
       to you under the Apache License, Version 2.0 (the
       "License"); you may not use this file except in compliance
       with the License.  You may obtain a copy of the License at

         http://www.apache.org/licenses/LICENSE-2.0

       Unless required by applicable law or agreed to in writing,
       software distributed under the License is distributed on an
       "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
       KIND, either express or implied.  See the License for the
       specific language governing permissions and limitations
       under the License.
*/

// GENERATED FILE! DO NOT EDIT!

apply plugin: 'android'

buildscript {
    repositories {
        mavenCentral()
    }

    // Switch the Android Gradle plugin version requirement depending on the
    // installed version of Gradle. This dependency is documented at
    // http://tools.android.com/tech-docs/new-build-system/version-compatibility
    // and https://issues.apache.org/jira/browse/CB-8143
    dependencies {
        classpath 'com.android.tools.build:gradle:1.5.0'
    }
   }

// Allow plugins to declare Maven dependencies via build-extras.gradle.
repositories {
    mavenCentral()
}

task wrapper(type: Wrapper) {
    gradleVersion = '2.8'
}

// Configuration properties. Set these via environment variables, build-extras.gradle, or gradle.properties.
// Refer to: http://www.gradle.org/docs/current/userguide/tutorial_this_and_that.html
ext {
    apply from: 'CordovaLib/cordova.gradle'
    // The value for android.compileSdkVersion.
    if (!project.hasProperty('cdvCompileSdkVersion')) {
        cdvCompileSdkVersion = null;
    }
    // The value for android.buildToolsVersion.
    if (!project.hasProperty('cdvBuildToolsVersion')) {
        cdvBuildToolsVersion = null;
    }
    // Sets the versionCode to the given value.
    if (!project.hasProperty('cdvVersionCode')) {
        cdvVersionCode = null
    }
    // Sets the minSdkVersion to the given value.
    if (!project.hasProperty('cdvMinSdkVersion')) {
        cdvMinSdkVersion = null
    }
    // Whether to build architecture-specific APKs.
    if (!project.hasProperty('cdvBuildMultipleApks')) {
        cdvBuildMultipleApks = null
    }
    // .properties files to use for release signing.
    if (!project.hasProperty('cdvReleaseSigningPropertiesFile')) {
        cdvReleaseSigningPropertiesFile = null
    }
    // .properties files to use for debug signing.
    if (!project.hasProperty('cdvDebugSigningPropertiesFile')) {
        cdvDebugSigningPropertiesFile = null
    }
    // Set by build.js script.
    if (!project.hasProperty('cdvBuildArch')) {
        cdvBuildArch = null
    }

    // Plugin gradle extensions can append to this to have code run at the end.
    cdvPluginPostBuildExtras = []
}

// PLUGIN GRADLE EXTENSIONS START
// PLUGIN GRADLE EXTENSIONS END

def hasBuildExtras = file('build-extras.gradle').exists()
if (hasBuildExtras) {
    apply from: 'build-extras.gradle'
}

// Set property defaults after extension .gradle files.
if (ext.cdvCompileSdkVersion == null) {
    ext.cdvCompileSdkVersion = privateHelpers.getProjectTarget()
}
if (ext.cdvBuildToolsVersion == null) {
    ext.cdvBuildToolsVersion = privateHelpers.findLatestInstalledBuildTools()
}
if (ext.cdvDebugSigningPropertiesFile == null && file('debug-signing.properties').exists()) {
    ext.cdvDebugSigningPropertiesFile = 'debug-signing.properties'
}
if (ext.cdvReleaseSigningPropertiesFile == null && file('release-signing.properties').exists()) {
    ext.cdvReleaseSigningPropertiesFile = 'release-signing.properties'
}

// Cast to appropriate types.
ext.cdvBuildMultipleApks = cdvBuildMultipleApks == null ? false : cdvBuildMultipleApks.toBoolean();
ext.cdvMinSdkVersion = cdvMinSdkVersion == null ? null : Integer.parseInt('' + cdvMinSdkVersion)
ext.cdvVersionCode = cdvVersionCode == null ? null : Integer.parseInt('' + cdvVersionCode)

def computeBuildTargetName(debugBuild) {
    def ret = 'assemble'
    if (cdvBuildMultipleApks && cdvBuildArch) {
        def arch = cdvBuildArch == 'arm' ? 'armv7' : cdvBuildArch
        ret += '' + arch.toUpperCase().charAt(0) + arch.substring(1);
    }
    return ret + (debugBuild ? 'Debug' : 'Release')
}

// Make cdvBuild a task that depends on the debug/arch-sepecific task.
task cdvBuildDebug
cdvBuildDebug.dependsOn {
    return computeBuildTargetName(true)
}

task cdvBuildRelease
cdvBuildRelease.dependsOn {
    return computeBuildTargetName(false)
}

task cdvPrintProps << {
    println('cdvCompileSdkVersion=' + cdvCompileSdkVersion)
    println('cdvBuildToolsVersion=' + cdvBuildToolsVersion)
    println('cdvVersionCode=' + cdvVersionCode)
    println('cdvMinSdkVersion=' + cdvMinSdkVersion)
    println('cdvBuildMultipleApks=' + cdvBuildMultipleApks)
    println('cdvReleaseSigningPropertiesFile=' + cdvReleaseSigningPropertiesFile)
    println('cdvDebugSigningPropertiesFile=' + cdvDebugSigningPropertiesFile)
    println('cdvBuildArch=' + cdvBuildArch)
    println('computedVersionCode=' + android.defaultConfig.versionCode)
    android.productFlavors.each { flavor ->
        println('computed' + flavor.name.capitalize() + 'VersionCode=' + flavor.versionCode)
    }
}

android {
    sourceSets {
        main {
            manifest.srcFile 'AndroidManifest.xml'
            java.srcDirs = ['src']
            resources.srcDirs = ['src']
            aidl.srcDirs = ['src']
            renderscript.srcDirs = ['src']
            res.srcDirs = ['res']
            assets.srcDirs = ['assets']
            jniLibs.srcDirs = ['libs']
        }
    }

    defaultConfig {
        versionCode cdvVersionCode ?: Integer.parseInt("" + privateHelpers.extractIntFromManifest("versionCode") + "0")
        applicationId privateHelpers.extractStringFromManifest("package")

        multiDexEnabled true

        if (cdvMinSdkVersion != null) {
            minSdkVersion cdvMinSdkVersion
        }
    }

    lintOptions {
      abortOnError false;
    }

    compileSdkVersion cdvCompileSdkVersion
    buildToolsVersion cdvBuildToolsVersion

    if (Boolean.valueOf(cdvBuildMultipleApks)) {
        productFlavors {
            armv7 {
                versionCode defaultConfig.versionCode + 2
                ndk {
                    abiFilters "armeabi-v7a", ""
                }
            }
            x86 {
                versionCode defaultConfig.versionCode + 4
                ndk {
                    abiFilters "x86", ""
                }
            }
            all {
                ndk {
                    abiFilters "all", ""
                }
            }
        }
    } else if (!cdvVersionCode) {
      def minSdkVersion = cdvMinSdkVersion ?: privateHelpers.extractIntFromManifest("minSdkVersion")
      // Vary versionCode by the two most common API levels:
      // 14 is ICS, which is the lowest API level for many apps.
      // 20 is Lollipop, which is the lowest API level for the updatable system webview.
      if (minSdkVersion >= 20) {
        defaultConfig.versionCode += 9
      } else if (minSdkVersion >= 14) {
        defaultConfig.versionCode += 8
      }
    }

    compileOptions {
        sourceCompatibility JavaVersion.VERSION_1_6
        targetCompatibility JavaVersion.VERSION_1_6
    }

    if (cdvReleaseSigningPropertiesFile) {
        signingConfigs {
            release {
                // These must be set or Gradle will complain (even if they are overridden).
                keyAlias = ""
                keyPassword = "__unset" // And these must be set to non-empty in order to have the signing step added to the task graph.
                storeFile = null
                storePassword = "__unset"
            }
        }
        buildTypes {
            release {
                signingConfig signingConfigs.release
            }
        }
        addSigningProps(cdvReleaseSigningPropertiesFile, signingConfigs.release)
    }
    if (cdvDebugSigningPropertiesFile) {
        addSigningProps(cdvDebugSigningPropertiesFile, signingConfigs.debug)
    }
}

configurations {
    all*.exclude group: 'com.android.support', module: 'support-v4'
}

dependencies {
    compile 'com.android.support:multidex:1.0.1'
    compile fileTree(include: '*.jar', dir: 'libs')
    // SUB-PROJECT DEPENDENCIES START
    debugCompile project(path: 'CordovaLib', configuration: 'debug')
    releaseCompile project(path: 'CordovaLib', configuration: 'release')
    // SUB-PROJECT DEPENDENCIES END
    compile files('libs/android-support-v4.jar')
    compile files('libs/classes.jar')
    compile files('libs/com.datecs.api.jar')
    compile files('libs/gson-2.2.4.jar')
    compile files('libs/Wallet-E-sdk-1.8.0.jar')
    compile files('libs/Wallet-E-sdk-1.8.0-javadoc.jar')
}

def promptForReleaseKeyPassword() {
    if (!cdvReleaseSigningPropertiesFile) {
        return;
    }
    if ('__unset'.equals(android.signingConfigs.release.storePassword)) {
        android.signingConfigs.release.storePassword = privateHelpers.promptForPassword('Enter key store password: ')
    }
    if ('__unset'.equals(android.signingConfigs.release.keyPassword)) {
        android.signingConfigs.release.keyPassword = privateHelpers.promptForPassword('Enter key password: ');
    }
}

gradle.taskGraph.whenReady { taskGraph ->
    taskGraph.getAllTasks().each() { task ->
        if (task.name == 'validateReleaseSigning') {
            promptForReleaseKeyPassword()
        }
    }
}

def addSigningProps(propsFilePath, signingConfig) {
    def propsFile = file(propsFilePath)
    def props = new Properties()
    propsFile.withReader { reader ->
        props.load(reader)
    }

    def storeFile = new File(props.get('key.store') ?: privateHelpers.ensureValueExists(propsFilePath, props, 'storeFile'))
    if (!storeFile.isAbsolute()) {
        storeFile = RelativePath.parse(true, storeFile.toString()).getFile(propsFile.getParentFile())
    }
    if (!storeFile.exists()) {
        throw new FileNotFoundException('Keystore file does not exist: ' + storeFile.getAbsolutePath())
    }
    signingConfig.keyAlias = props.get('key.alias') ?: privateHelpers.ensureValueExists(propsFilePath, props, 'keyAlias')
    signingConfig.keyPassword = props.get('keyPassword', props.get('key.alias.password', signingConfig.keyPassword))
    signingConfig.storeFile = storeFile
    signingConfig.storePassword = props.get('storePassword', props.get('key.store.password', signingConfig.storePassword))
    def storeType = props.get('storeType', props.get('key.store.type', ''))
    if (!storeType) {
        def filename = storeFile.getName().toLowerCase();
        if (filename.endsWith('.p12') || filename.endsWith('.pfx')) {
            storeType = 'pkcs12'
        } else {
            storeType = signingConfig.storeType // "jks"
        }
    }
    signingConfig.storeType = storeType
}

for (def func : cdvPluginPostBuildExtras) {
    func()
}

// This can be defined within build-extras.gradle as:
//     ext.postBuildExtras = { ... code here ... }
if (hasProperty('postBuildExtras')) {
    postBuildExtras()
}enter code here

Follow the below URL, Cordova documentaion has listed the steps to upgrade Cordova version.

Upgrade Cordova Version

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