Split the Android platform java logic into an Android library module (lib) and an application module (app).

The application module `app` serves double duties of providing the prebuilt Godot binaries ('android_debug.apk', 'android_release.apk') and the Godot custom build template ('android_source.zip').

platform/android/java/app/AndroidManifest.xml

@@ -0,0 +1,65 @@
+<?xml version="1.0" encoding="utf-8"?>
+<manifest xmlns:android="http://schemas.android.com/apk/res/android"
+    xmlns:tools="http://schemas.android.com/tools"
+    package="com.godot.game"
+    android:versionCode="1"
+    android:versionName="1.0"
+    android:installLocation="auto" >
+
+    <!-- Adding custom text to the manifest is fine, but do it outside the custom USER and APPLICATION BEGIN/END comments, -->
+    <!-- as that gets rewritten. -->
+
+    <supports-screens
+        android:smallScreens="true"
+        android:normalScreens="true"
+        android:largeScreens="true"
+        android:xlargeScreens="true" />
+
+    <!-- glEsVersion is modified by the exporter, changing this value here has no effect. -->
+    <uses-feature
+        android:glEsVersion="0x00020000"
+        android:required="true" />
+
+<!-- Custom user permissions XML added by add-ons. It's recommended to add them from the export preset, though. -->
+<!--CHUNK_USER_PERMISSIONS_BEGIN-->
+<!--CHUNK_USER_PERMISSIONS_END-->
+
+    <!-- Any tag in this line after android:icon will be erased when doing custom builds. -->
+    <!-- If you want to add tags manually, do before it. -->
+    <application
+        android:label="@string/godot_project_name_string"
+        android:allowBackup="false"
+        tools:ignore="GoogleAppIndexingWarning"
+        android:icon="@drawable/icon" >
+
+        <!-- The following metadata values are replaced when Godot exports, modifying them here has no effect. -->
+        <!-- Do these changes in the export preset. Adding new ones is fine. -->
+
+        <!-- XR mode metadata. This is modified by the exporter based on the selected xr mode. DO NOT CHANGE the values here. -->
+        <meta-data
+            android:name="xr_mode_metadata_name"
+            android:value="xr_mode_metadata_value" />
+
+        <activity
+            android:name=".GodotApp"
+            android:label="@string/godot_project_name_string"
+            android:theme="@android:style/Theme.Black.NoTitleBar.Fullscreen"
+            android:launchMode="singleTask"
+            android:screenOrientation="landscape"
+            android:configChanges="orientation|keyboardHidden|screenSize|smallestScreenSize|density|keyboard|navigation|screenLayout|uiMode"
+            android:resizeableActivity="false"
+            tools:ignore="UnusedAttribute" >
+
+            <intent-filter>
+                <action android:name="android.intent.action.MAIN" />
+                <category android:name="android.intent.category.LAUNCHER" />
+            </intent-filter>
+        </activity>
+
+<!-- Custom application XML added by add-ons. -->
+<!--CHUNK_APPLICATION_BEGIN-->
+<!--CHUNK_APPLICATION_END-->
+
+    </application>
+
+</manifest>

platform/android/java/app/build.gradle

@@ -0,0 +1,121 @@
+// Gradle build config for Godot Engine's Android port.
+//
+// Do not remove/modify comments ending with BEGIN/END, they are used to inject
+// addon-specific configuration.
+apply from: 'config.gradle'
+
+buildscript {
+    apply from: 'config.gradle'
+
+    repositories {
+        google()
+        jcenter()
+//CHUNK_BUILDSCRIPT_REPOSITORIES_BEGIN
+//CHUNK_BUILDSCRIPT_REPOSITORIES_END
+    }
+    dependencies {
+        classpath libraries.androidGradlePlugin
+//CHUNK_BUILDSCRIPT_DEPENDENCIES_BEGIN
+//CHUNK_BUILDSCRIPT_DEPENDENCIES_END
+    }
+}
+
+apply plugin: 'com.android.application'
+
+allprojects {
+    repositories {
+        mavenCentral()
+        google()
+        jcenter()
+//CHUNK_ALLPROJECTS_REPOSITORIES_BEGIN
+//CHUNK_ALLPROJECTS_REPOSITORIES_END
+    }
+}
+
+dependencies {
+    if (rootProject.findProject(":lib")) {
+        implementation project(":lib")
+    } else {
+        // Custom build mode. In this scenario this project is the only one around and the Godot
+        // library is available through the pre-generated godot-lib.*.aar android archive files.
+        debugImplementation fileTree(dir: 'libs/debug', include: ['*.jar', '*.aar'])
+        releaseImplementation fileTree(dir: 'libs/release', include: ['*.jar', '*.aar'])
+    }
+//CHUNK_DEPENDENCIES_BEGIN
+//CHUNK_DEPENDENCIES_END
+}
+
+android {
+    compileSdkVersion versions.compileSdk
+    buildToolsVersion versions.buildTools
+
+    defaultConfig {
+        // Feel free to modify the application id to your own.
+        applicationId "com.godot.game"
+        minSdkVersion versions.minSdk
+        targetSdkVersion versions.targetSdk
+//CHUNK_ANDROID_DEFAULTCONFIG_BEGIN
+//CHUNK_ANDROID_DEFAULTCONFIG_END
+    }
+
+    lintOptions {
+        abortOnError false
+        disable 'MissingTranslation', 'UnusedResources'
+    }
+
+    packagingOptions {
+        exclude 'META-INF/LICENSE'
+        exclude 'META-INF/NOTICE'
+    }
+
+    // Both signing and zip-aligning will be done at export time
+    buildTypes.all { buildType ->
+        buildType.zipAlignEnabled false
+        buildType.signingConfig null
+    }
+
+    sourceSets {
+        main {
+            manifest.srcFile 'AndroidManifest.xml'
+            java.srcDirs = [
+                    'src'
+//DIR_SRC_BEGIN
+//DIR_SRC_END
+            ]
+            res.srcDirs = [
+                    'res'
+//DIR_RES_BEGIN
+//DIR_RES_END
+            ]
+            aidl.srcDirs = [
+                    'aidl'
+//DIR_AIDL_BEGIN
+//DIR_AIDL_END
+            ]
+            assets.srcDirs = [
+                    'assets'
+//DIR_ASSETS_BEGIN
+//DIR_ASSETS_END
+            ]
+        }
+        debug.jniLibs.srcDirs = [
+                'libs/debug'
+//DIR_JNI_DEBUG_BEGIN
+//DIR_JNI_DEBUG_END
+        ]
+        release.jniLibs.srcDirs = [
+                'libs/release'
+//DIR_JNI_RELEASE_BEGIN
+//DIR_JNI_RELEASE_END
+        ]
+    }
+
+    applicationVariants.all { variant ->
+        variant.outputs.all { output ->
+            output.outputFileName = "android_${variant.name}.apk"
+        }
+    }
+}
+
+//CHUNK_GLOBAL_BEGIN
+//CHUNK_GLOBAL_END

platform/android/java/app/config.gradle

@@ -0,0 +1,12 @@
+ext.versions = [
+        androidGradlePlugin : '3.4.2',
+        compileSdk : 28,
+        minSdk : 18,
+        targetSdk : 28,
+        buildTools : '28.0.3',
+
+]
+
+ext.libraries = [
+        androidGradlePlugin : "com.android.tools.build:gradle:$versions.androidGradlePlugin"
+]

platform/android/java/app/src/com/godot/game/GodotApp.java

@@ -0,0 +1,10 @@
+package com.godot.game;
+
+import org.godotengine.godot.Godot;
+
+/**
+ * Template activity for Godot Android custom builds.
+ * Feel free to extend and modify this class for your custom logic.
+ */
+public class GodotApp extends Godot {
+}