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Android Studio keeps generating Eclipse-like files

I'm using Android Studio 3.0.1 and I have noticed that for one of my projects (only this one) it generates .project files and a bin directory like Eclipse does (I suppose).
The project was created in AS 3.0.1 and it was not migrated from Eclipse or anything like this. It also doesn't use any fancy Gradle plugins or dependencies - just the generated ones (AppCompat + Kotlin).
Do you have any idea why it does so?
Also, when I was trying to prepare a minimal project for reproduction, I noticed that the problem disappears just by copy-pasting the whole project directory so there's probably no point in sharing it with you.
Using two project copies (let's call them original and copy) I was able to find out that when I close Android Studio and clean both copies using git clean -xfd
copy has no issues when opened - no Eclipse-like files
original still has the issue when opened (files get generated)
diff -r before opening them (so just after git clean) gives only this:
Binary files ../PWTA_Proj2/.git/index and ./.git/index differ
both of them make Android Studio show an error like this when opened:
Unsupported Modules Detected: Compilation is not supported for following modules: PWTA_Proj2. Unfortunately you can't have non-Gradle Java modules and Android-Gradle modules in one project.
Despite of the error I can build the project normally. Also I don't have any non-Gradle modules - the project is very simple and generated by AS. The only less common thing is that the project contains a few AIDL files.
Edit #1: Gradle files:
top-level build.gradle:
// Top-level build file where you can add configuration options common to all sub-projects/modules.
buildscript {
ext.kotlin_version = '1.2.0'
repositories {
google()
jcenter()
}
dependencies {
classpath 'com.android.tools.build:gradle:3.0.1'
classpath "org.jetbrains.kotlin:kotlin-gradle-plugin:$kotlin_version"
// NOTE: Do not place your application dependencies here; they belong
// in the individual module build.gradle files
}
}
allprojects {
repositories {
google()
jcenter()
}
}
task clean(type: Delete) {
delete rootProject.buildDir
}
top-level settings.gradle:
include ':app'
app module build.gradle:
apply plugin: 'com.android.application'
apply plugin: 'kotlin-android'
apply plugin: 'kotlin-android-extensions'
android {
compileSdkVersion 27
buildToolsVersion '27.0.3'
defaultConfig {
final appId = "com.azabost.pwta.proj2"
applicationId appId
minSdkVersion 25
targetSdkVersion 27
versionCode 1
versionName "1.0"
testInstrumentationRunner "android.support.test.runner.AndroidJUnitRunner"
manifestPlaceholders.tspProcessName = appId + ".tsp"
}
buildTypes {
release {
minifyEnabled false
proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
}
}
}
dependencies {
implementation fileTree(dir: 'libs', include: ['*.jar'])
implementation"org.jetbrains.kotlin:kotlin-stdlib-jre7:$kotlin_version"
implementation 'com.android.support:appcompat-v7:27.0.2'
testImplementation 'junit:junit:4.12'
androidTestImplementation 'com.android.support.test:runner:1.0.1'
androidTestImplementation 'com.android.support.test.espresso:espresso-core:3.0.1'
}

java.util.zip.ZipException: duplicate entry: javax/inject/Inject.class

I have seen similar responses to the below question. Sorry but i could not fixed it out trying multiple things so I am asking it again.
Whenever I am trying to build my app, the gradle build throws me the below error stating ...due to duplicate entry of javax/Inject class.
This only occurred when I am trying to put compile 'org.glassfish.jersey.containers:jersey-container-jdk-http:2.9' in my build.gradle file; This package is necessary for javax.ws.rs.* services.
I tried running the gradlew clean command in my root directory, it says that build is successful but when I am building my application again it started throwing the error again.
Can you please help on the below error:
*Error:Execution failed for task ':app:transformClassesWithJarMergingForDebug'.
> com.android.build.api.transform.TransformException: java.util.zip.ZipException: duplicate entry: javax/inject/Inject.class*
Below is my app gradle file:
apply plugin: 'com.android.application'
android {
compileSdkVersion 23
buildToolsVersion "23.0.3"
defaultConfig {
applicationId "com.usfca.studentrecordsverifycation"
minSdkVersion 17
targetSdkVersion 23
versionCode 1
versionName "1.0"
// Enabling multidex support.
multiDexEnabled true
}
buildTypes {
release {
minifyEnabled false
proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
}
}
}
repositories {
maven { url 'http://repo1.maven.org/maven2' }
maven { url 'http://maven.restlet.com' }
maven { url 'https://maven.java.net/content/repositories/releases/' }
maven { url 'http://download.java.net/maven/2/' }
maven { url 'http://download.java.net/maven/1' }
}
dependencies {
compile fileTree(include: ['*.jar'], dir: 'libs')
testCompile 'junit:junit:4.12'
compile 'com.android.support:appcompat-v7:23.3.0'
compile 'com.android.support:design:23.3.0'
compile 'com.android.support:multidex:1.0.1'
compile 'log4j:log4j:1.2.17'
compile 'com.google.code.gson:gson:2.2.4'
compile 'com.madgag:sc-light-jdk15on:1.47.0.3'
compile 'com.cloudinary:cloudinary-http44:1.4.5'
compile 'org.glassfish.jersey.containers:jersey-container-jdk-http:2.9'
compile 'commons-lang:commons-lang:2.6'
}
Below is my Project gradle:
buildscript {
repositories {
jcenter()
}
dependencies {
classpath 'com.android.tools.build:gradle:2.1.0'
// NOTE: Do not place your application dependencies here; they belong
// in the individual module build.gradle files
}
}
allprojects {
repositories {
jcenter()
}
}
task clean(type: Delete) {
delete rootProject.buildDir
}

Ok so I created a sample project with all those dependencies and I got a different error.
So if you are still getting the ZipException error, you have some jars in your lib folder that we are not aware of?
Here's the error I got:
Execution failed for task ':app:transformResourcesWithMergeJavaResForDebug'.
> com.android.build.api.transform.TransformException: com.android.builder.packaging.DuplicateFileException: Duplicate files copied in APK META-INF/LICENSE
If you are getting a similar error, all you need to do is add the following to your build.gradle:
android {
defaultConfig {
...
}
buildTypes {
....
}
packagingOptions {
exclude 'META-INF/LICENSE'
}
}
If this doesn't make any difference, do you have any jar libraries in your project? If so, we need to see the list.
EDIT:
I can't know for sure if it will work because I am not getting the same error. In your dependencies, change to this:
compile ('org.glassfish.jersey.containers:jersey-container-jdk-http:2.9') {
exclude group: 'javax.inject', module: 'javax.inject'
}

This error means that the class javax.inject.Inject is being included twice in your apk when the dexer runs. That is, this exact same class is coming from 2 different dependencies. One of them is probably org.glassfish.jersey.containers:jersey-container-jdk-http:2.9 because it happens after you added it.
If you CMD+O (jump to class) on Android Studio, you should be able to see the 2 versions of this class and see where they are coming from. Make sure you select the checkbox that allows it to show classes included from your dependencies. Once you open them, hover over the file tab and you'll see a tooltip with the artifact name. That is gonna be the dependency that's including that class.
Hope it makes sense.

Android Release Build

I was facing a problem earlier this week. When I tried to do the Android release build it seemed to show the following error --
Error:Execution failed for task ':app:transformClassesWithJarMergingForRelease'.
com.android.build.api.transform.TransformException: java.util.zip.ZipException: duplicate entry: com/google/android/gms/internal/zzjm.class
I was wondering how I got this error and how to fix it. It seems as if the problem was inside the build.gradle files. Here they are --
App Level -
apply plugin: 'com.android.application'
android {
compileSdkVersion 23
buildToolsVersion "23.0.2"
defaultConfig {
applicationId "com.unknown.app"
minSdkVersion 13
targetSdkVersion 23
versionCode 20
versionName "2.34"
multiDexEnabled true
}
buildTypes {
release {
minifyEnabled false
proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
}
}
}
dependencies {
compile fileTree(dir: 'libs', include: ['*.jar'])
compile project(':BaseGameUtils')
testCompile 'junit:junit:4.12'
compile 'com.android.support:appcompat-v7:23.4.0'
compile 'com.google.firebase:firebase-ads:9.0.2'
compile ('com.google.android.gms:play-services:9.0.2'){
exclude group: 'com.google.android.gms.play-services-ads'
}
compile project(path: ':BaseGameUtils')
}
apply plugin: 'com.google.gms.google-services'
Here is the top level --
// Top-level build file where you can add configuration options common to all sub-projects/modules.
buildscript {
repositories {
jcenter()
}
dependencies {
classpath 'com.android.tools.build:gradle:2.1.2'
classpath 'com.google.gms:google-services:3.0.0'
// NOTE: Do not place your application dependencies here; they belong
// in the individual module build.gradle files
}
}
allprojects {
repositories {
jcenter()
}
}
task clean(type: Delete) {
delete rootProject.buildDir
}
Thanks for all help. I have been having this issue for a little while. I could not find the answer in any other stack overflow questions. Thanks Again.

the error explains itself, it means that it found two libraries which are the same
compile 'com.google.android.gms:play-services:9.0.2'
compile 'com.google.android.gms:play-services-ads:9.0.2'
compile 'com.google.android.gms:play-services-identity:9.0.2'
compile 'com.google.android.gms:play-services-gcm:9.0.2'
by including com.google.android.gms:play-services:9.0.2 you are actually including all the play-service libraries, please remove it and you should be fine or remove the others "below it".

you are including the
'com.google.firebase:firebase-ads:9.0.2'
and
'com.google.android.gms:play-services-ads:9.0.2'
but firebase already includes the second library so you don't have to include this one just use the ads library from firebase

It seems as if the BaseGameUtils module was causing the problem. I am not sure why but reomving it, and replacing the BaseGameUtils for some reason did the trick, and the error did not show anymore. Thanks for all the help along the way of figuring out the issue.

Duplicate files copied in APK META-INF

hi im new in android development, i am trying to build my apk but i got this erorr. and i update my gradle and i got duplicate copy. how can i fix this error?
Error:Execution failed for task ':app:transformResourcesWithMergeJavaResForDebug'.
> com.android.build.api.transform.TransformException: com.android.builder.packaging.DuplicateFileException: Duplicate files copied in APK META-INF/maven/com.squareup.okhttp/okhttp/pom.properties
File1: C:\Users\Toshiba\.gradle\caches\modules-2\files-2.1\com.squareup.okhttp\okhttp\2.0.0\4c8d1536dba3812cc1592090dc20c47a4ed3c35e\okhttp-2.0.0.jar
File2: C:\Users\Toshiba\.gradle\caches\modules-2\files-2.1\com.crashlytics.android\crashlytics\1.1.13\e821eafa1bf489a26bdb71f95078c26785b37a1\crashlytics-1.1.13.jar
and here's my build.gradle is this the error comes?
buildscript {
repositories {
maven { url 'http://download.crashlytics.com/maven' }
}
dependencies {
classpath 'com.crashlytics.tools.gradle:crashlytics-gradle:1.+'
}
}
apply plugin: 'com.android.application'
apply plugin: 'crashlytics'
android {
compileSdkVersion 20
buildToolsVersion "20.0.0"
defaultConfig {
applicationId "com.mymonas.ngobrol"
minSdkVersion 14
targetSdkVersion 20
versionCode 1
versionName "0.9.0.68"
}
buildTypes {
release {
minifyEnabled false
proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
}
}
}
repositories {
mavenCentral()
maven { url 'http://download.crashlytics.com/maven' }
}
dependencies {
compile fileTree(dir: 'libs', include: ['*.jar'], exclude: 'android-support-v4.jar')
compile project('libs:floatlabel')
compile 'com.android.support:support-v4:21.0.0'
compile 'com.android.support:support-v13:21.0.0'
compile 'com.squareup.retrofit:retrofit:1.7.0'
compile 'com.squareup.okhttp:okhttp-urlconnection:2.0.0'
compile 'com.squareup.okhttp:okhttp:2.0.0'
compile 'com.github.dmytrodanylyk.android-process-button:library:1.0.1'
compile 'com.google.android.gms:play-services:6.1.11'
compile 'com.viewpagerindicator:library:2.4.1#aar'
compile 'com.astuetz:pagerslidingtabstrip:1.0.1'
compile 'com.nostra13.universalimageloader:universal-image-loader:1.9.3'
compile 'com.makeramen:roundedimageview:1.3.0'
compile 'com.andreabaccega:android-form-edittext:1.1.0#aar'
compile 'com.crashlytics.android:crashlytics:1.+'
}

I had the same or at least a very similar problem today with our React Native app. The problem was only on my Mac though. The only plausible explanation we could think of was that I updated a bunch of Android Studio tools and then gradle couldn't build properly with our dependencies. Anyways after excluding the pom.properties and pom.xml from okhttp I kept getting the same error but it turns out that I just had to exclude even more files. This is my complete packagingOptions in build.gradle:
packagingOptions {
exclude 'META-INF/maven/com.squareup.okhttp3/okhttp/pom.properties'
exclude 'META-INF/maven/com.squareup.okio/okio/pom.xml'
exclude 'META-INF/maven/com.squareup.okhttp3/okhttp/pom.xml'
exclude 'META-INF/maven/com.squareup.okio/okio/pom.properties'
}

to solve your problem please add this to your build gradle
packagingOptions {
exclude 'META-INF/pom.properties' /*OR*/ 'META-INF/maven/com.squareup.okhttp/okhttp/pom.properties
}

It seems like okhttp and crashlytics don't work together in newer gradle versions (2.10 in my case). I fixed this by updating the crashlytics to a newer version (which is now called Fabric).

packagingOptions
{
exclude 'META-INF/maven/com.squareup.okhttp/okhttp/pom.properties
exclude 'META-INF/maven/com.squareup.okhttp/okhttp/pom.xml'
}
Please check for correct path "com.squareup.okhttp/okhttp/pom.properties" in your errorlog.

Android gradle :app:packageDebug FAILED: class org.bouncycastle.asn1.ASN1Primitive overrides final method equals

I'm new to Android and I can't get my first app to run. Whenever I try, it's throwing this error:
Android gradle :app:packageDebug FAILED: class org.bouncycastle.asn1.ASN1Primitive overrides final method equals.
I googled it and I found many questions there. As many said, this problem is probably due to the fact that I have multiple dependencies on BouncyCastle in my project. I tryed to remove the .gradle folder both in my project and in my local folder so I could download again the jars from the repository but nothing has changed. I also double checked that my JAVA_HOME is set and it's pointing to a 1.7 version. I tryed to gradle :app:clean and gradle :app:dependencies to see if I was missing something but still... I can't see any dependency from BouncyCastle... Can anybody help me?
Also, this problem occured without me changing any code... The app successfully worked yesterday and now is giving me this error... I don't get it. Thank you.
EDIT
gradle.build
Top-level:
// Top-level build file where you can add configuration options common to all sub-projects/modules.
buildscript {
repositories {
jcenter()
}
dependencies {
classpath 'com.android.tools.build:gradle:1.1.0'
// NOTE: Do not place your application dependencies here; they belong
// in the individual module build.gradle files
}
}
allprojects {
repositories {
jcenter()
}
}
Module app:
apply plugin: 'com.android.application'
android {
compileSdkVersion 21
buildToolsVersion "21.1.2"
defaultConfig {
applicationId "com.example.aurasphere.provaactionbar"
minSdkVersion 11
targetSdkVersion 21
versionCode 1
versionName "1.0"
}
buildTypes {
release {
minifyEnabled false
proguardFiles getDefaultProguardFile('proguard-android.txt'), 'proguard-rules.pro'
}
}
}
dependencies {
compile fileTree(dir: 'libs', include: ['*.jar'])
compile 'com.android.support:appcompat-v7:22.0.0'
compile 'com.google.android.gms:play-services:7.0.0'
compile project(':volley')
compile files('libs/gson-2.2.2.jar')
}
Module volley:
buildscript {
repositories {
mavenCentral()
}
dependencies {
classpath 'com.android.tools.build:gradle:0.14.+'
}
}
apply plugin: 'com.android.library'
android {
compileSdkVersion 19
buildToolsVersion = '21.1.0'
}
apply from: 'rules.gradle'
rules.gradle for module volley:
apply plugin: 'com.android.library'

I've solved this problem myself just by changing the JDK I was using from x32 to x64 and now is compiling correctly.