diff --git a/libraries/commonConfiguration.gradle b/libraries/commonConfiguration.gradle
index c8071ec9124..85360c3d32b 100644
--- a/libraries/commonConfiguration.gradle
+++ b/libraries/commonConfiguration.gradle
@@ -5,14 +5,14 @@ String jdkPath(String version) {
     return path
 }
 
-ext {
-    JDK_16 = jdkPath("1.6")
-    JDK_17 = jdkPath("1.7")
-    JDK_18 = jdkPath("1.8")
-    distDir = file("$kotlin_root/dist")
-    distLibDir = file("$kotlin_root/dist/kotlinc/lib")
-    bootstrapCompilerFile = file("$distDir/kotlin-compiler-for-maven.jar")
-}
+//ext {
+//    JDK_16 = jdkPath("1.6")
+//    JDK_17 = jdkPath("1.7")
+//    JDK_18 = jdkPath("1.8")
+//    distDir = file("$kotlin_root/dist")
+//    distLibDir = file("$kotlin_root/dist/kotlinc/lib")
+//    bootstrapCompilerFile = file("$distDir/kotlin-compiler-for-maven.jar")
+//}
 
 ext.configureJvmProject = { Project project ->
     project.configure(project) {
@@ -159,9 +159,11 @@ ext.configurePublishing = { Project project ->
 
 ext.createPreprocessorTask = { Project project, def name, def sourceDir, def targetDir, def profile = "JS" ->
     return project.tasks.create("preprocessSources$name", JavaExec) {
+//        dependsOn(rootProject.prepareBootstrap)
         inputs.dir(sourceDir)
         outputs.dir(targetDir)
-        classpath = project.files(bootstrapCompilerFile)
+        classpath = rootProject.configurations.bootstrapCompile
+//        classpath = project.files(bootstrapCompilerFile)
         main = "org.jetbrains.kotlin.preprocessor.PreprocessorCLI"
         args = [sourceDir, targetDir, profile]
     }
@@ -170,13 +172,15 @@ ext.createPreprocessorTask = { Project project, def name, def sourceDir, def tar
 ext.createScriptTask = { Project project, def name, Closure<JavaExec> configureClosure = null ->
     JavaExec task = project.tasks.create(name, JavaExec)
     return project.configure(task) {
-        classpath = project.configurations.scriptCompile
+//        dependsOn(rootProject.prepareBootstrap)
+        classpath = rootProject.configurations.scriptCompile
+        println(rootProject.configurations.scriptCompile.files)
         main = "org.jetbrains.kotlin.cli.jvm.K2JVMCompiler"
         args = [
                 "-script",
                 "-version",
                 "-no-stdlib",
-                "-cp", project.configurations.scriptRuntime.asPath]
+                "-cp", rootProject.configurations.scriptRuntime.asPath]
 
         if (configureClosure != null) {
             configureClosure.delegate = it
diff --git a/libraries/configureGradleTools.gradle b/libraries/configureGradleTools.gradle
new file mode 100644
index 00000000000..36663025076
--- /dev/null
+++ b/libraries/configureGradleTools.gradle
@@ -0,0 +1,36 @@
+
+configure([project(':kotlin-gradle-plugin'), project(':kotlin-allopen'), project(':kotlin-noarg')]) { project ->
+    apply plugin: 'com.gradle.plugin-publish'
+
+    if (project.hasProperty('publishPluginsVersion')) {
+        configurations.archives.artifacts.all {
+            version = project.getProperty('publishPluginsVersion')
+        }
+    }
+
+    if (project.hasProperty("${project.name}-jar")) {
+        println("Using pre-built artifact for ${project.name}")
+        configurations.archives.artifacts.clear()
+
+        artifacts {
+            archives(file(project.getProperty("${project.name}-jar"))) {
+                name project.name
+            }
+        }
+    }
+
+    publishPlugins.doFirst {
+        assert !kotlin_version.contains('SNAPSHOT')
+    }
+
+    pluginBundle {
+        website = 'https://kotlinlang.org/'
+        vcsUrl = 'https://github.com/JetBrains/kotlin/'
+        description = 'Kotlin plugins for Gradle'
+        tags = ['kotlin']
+
+        mavenCoordinates {
+            groupId = "org.jetbrains.kotlin"
+        }
+    }
+}
diff --git a/libraries/gradle/wrapper/gradle-wrapper.properties b/libraries/gradle/wrapper/gradle-wrapper.properties
deleted file mode 100644
index 8364dbbca1c..00000000000
--- a/libraries/gradle/wrapper/gradle-wrapper.properties
+++ /dev/null
@@ -1,6 +0,0 @@
-#Fri Apr 28 16:02:26 MSK 2017
-distributionBase=GRADLE_USER_HOME
-distributionPath=wrapper/dists
-zipStoreBase=GRADLE_USER_HOME
-zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-3.5-bin.zip
diff --git a/libraries/gradlePluginsConfiguration.gradle b/libraries/gradlePluginsConfiguration.gradle
new file mode 100644
index 00000000000..73ac0e9764e
--- /dev/null
+++ b/libraries/gradlePluginsConfiguration.gradle
@@ -0,0 +1,42 @@
+
+//task clean {
+//    doLast {
+//        delete "${buildDir}/repo"
+//    }
+//}
+
+configure([project(':kotlin-gradle-plugin'), project(':kotlin-allopen'), project(':kotlin-noarg')]) { project ->
+    apply plugin: 'com.gradle.plugin-publish'
+
+    if (project.hasProperty('publishPluginsVersion')) {
+        configurations.archives.artifacts.all {
+            version = project.getProperty('publishPluginsVersion')
+        }
+    }
+
+    if (project.hasProperty("${project.name}-jar")) {
+        println("Using pre-built artifact for ${project.name}")
+        configurations.archives.artifacts.clear()
+
+        artifacts {
+            archives(file(project.getProperty("${project.name}-jar"))) {
+                name project.name
+            }
+        }
+    }
+
+    publishPlugins.doFirst {
+        assert !kotlin_version.contains('SNAPSHOT')
+    }
+
+    pluginBundle {
+        website = 'https://kotlinlang.org/'
+        vcsUrl = 'https://github.com/JetBrains/kotlin/'
+        description = 'Kotlin plugins for Gradle'
+        tags = ['kotlin']
+
+        mavenCoordinates {
+            groupId = "org.jetbrains.kotlin"
+        }
+    }
+}
\ No newline at end of file
diff --git a/libraries/stdlib/build.gradle b/libraries/stdlib/build.gradle
index b69cfeb2c38..f57336ae826 100644
--- a/libraries/stdlib/build.gradle
+++ b/libraries/stdlib/build.gradle
@@ -9,7 +9,7 @@ sourceSets {
     annotations {
         if(!System.properties.'idea.active') {
             java {
-                srcDir "${rootDir}/../core/runtime.jvm/src"
+                srcDir "${rootDir}/core/runtime.jvm/src"
                 include 'org/jetbrains/annotations/**'
             }
             kotlin {
@@ -19,13 +19,13 @@ sourceSets {
     }
     builtins {
         java {
-            srcDir "${rootDir}/../core/builtins/src"
-            srcDir "${rootDir}/../core/runtime.jvm/src"
+            srcDir "${rootDir}/core/builtins/src"
+            srcDir "${rootDir}/core/runtime.jvm/src"
             exclude 'org/jetbrains/annotations/**'
         }
         kotlin {
-            srcDir "${rootDir}/../core/builtins/src"
-            srcDir "${rootDir}/../core/runtime.jvm/src"
+            srcDir "${rootDir}/core/builtins/src"
+            srcDir "${rootDir}/core/runtime.jvm/src"
             exclude 'org/jetbrains/annotations/**'
         }
     }
@@ -56,7 +56,8 @@ task originalStdlibJar(type: Jar) {
 
 jar {
     manifestAttributes(manifest, project, 'Main')
-    from("${rootDir}/../dist/builtins")
+    dependsOn ":core:builtins:serialize"
+    from("${rootDir}/dist/builtins")
     from sourceSets.builtins.output
 }
 
@@ -64,14 +65,14 @@ task distJar(type: Jar) {
     baseName = 'dist-kotlin-stdlib'
     version = null
     manifestAttributes(manifest, project, 'Main')
-    from("${rootDir}/../dist/builtins")
+    from("${rootDir}/dist/builtins")
     from sourceSets.annotations.output
     from sourceSets.builtins.output
     from sourceSets.main.output
 }
 
 sourcesJar {
-    from "${rootDir}/../core/builtins/native"
+    from "${rootDir}/core/builtins/native"
     from sourceSets.builtins.kotlin
 }
 
@@ -102,7 +103,7 @@ compileBuiltinsKotlin {
                 "-version",
                 "-Xallow-kotlin-package",
                 "-Xdump-declarations-to", "${buildDir}/runtime-declarations.json",
-                "-cp", "${rootDir}/../dist/builtins",
+                "-cp", "${rootDir}/dist/builtins",
                 "-module-name", "kotlin-runtime"
         ]
     }
diff --git a/libraries/stdlib/common/build.gradle b/libraries/stdlib/common/build.gradle
index 09b85a4fe02..809b227eec0 100644
--- a/libraries/stdlib/common/build.gradle
+++ b/libraries/stdlib/common/build.gradle
@@ -17,7 +17,11 @@ sourceSets {
 
 createPreprocessorTask(project, "Main", "${projectDir}/../src/kotlin", commonSrcDir)
 
-compileKotlinCommon.dependsOn preprocessSourcesMain
+compileKotlinCommon {
+    dependsOn preprocessSourcesMain
+//    dependsOn ":prepare:compiler:prepare-compiler-with-bootstrap-runtime"
+//    compilerJarFile = compilerJarWithBootstrapRuntime
+}
 
 /*
 // TODO: currently unsupported
diff --git a/libraries/stdlib/js/build.gradle b/libraries/stdlib/js/build.gradle
index 6b4fe8458be..fad1bc21249 100644
--- a/libraries/stdlib/js/build.gradle
+++ b/libraries/stdlib/js/build.gradle
@@ -13,8 +13,8 @@ def builtinsSrcDir = "${buildDir}/builtin-sources"
 def builtinsSrcDir2 = "${buildDir}/builtin-sources-for-builtins"
 def commonSrcDir = "${buildDir}/common-sources"
 def commonTestSrcDir = "${buildDir}/common-test-sources"
-def builtinsDir = "${rootDir}/../core/builtins"
-def jsLibrariesDir = "${rootDir}/../js/js.libraries"
+def builtinsDir = "${rootDir}/core/builtins"
+def jsLibrariesDir = "${rootDir}/js/js.libraries"
 def jsSrcDir = "${jsLibrariesDir}/src"
 def jsTestSrcDir = "${jsLibrariesDir}/test"
 def jsSrcJsDir = "${jsSrcDir}/js"
@@ -205,7 +205,7 @@ task mergedJar(type: Jar, dependsOn: classes) {
 
     // TODO: Use standard implementation title after js stdlib detector becomes more flexible
     Properties properties = new Properties()
-    new File("${rootDir}/../resources/kotlinManifest.properties").withInputStream {
+    new File("${rootDir}/resources/kotlinManifest.properties").withInputStream {
         properties.load(it)
     }
     manifest.attributes 'Implementation-Title' : properties."manifest.impl.title.kotlin.javascript.stdlib"
diff --git a/libraries/tools/gradle-tools/build.gradle b/libraries/tools/gradle-tools/build.gradle
index 9679923641d..323faa4339f 100644
--- a/libraries/tools/gradle-tools/build.gradle
+++ b/libraries/tools/gradle-tools/build.gradle
@@ -18,6 +18,7 @@ allprojects {
 }
 
 apply from: "${kotlin_root}/libraries/commonConfiguration.gradle"
+apply from: "${kotlin_root}/libraries/configureGradleTools.gradle"
 
 subprojects {
     repositories {
@@ -58,38 +59,3 @@ task clean {
     }
 }
 
-configure([project(':kotlin-gradle-plugin'), project(':kotlin-allopen'), project(':kotlin-noarg')]) { project ->
-    apply plugin: 'com.gradle.plugin-publish'
-
-    if (project.hasProperty('publishPluginsVersion')) {
-        configurations.archives.artifacts.all {
-            version = project.getProperty('publishPluginsVersion')
-        }
-    }
-
-    if (project.hasProperty("${project.name}-jar")) {
-        println("Using pre-built artifact for ${project.name}")
-        configurations.archives.artifacts.clear()
-
-        artifacts {
-            archives(file(project.getProperty("${project.name}-jar"))) {
-                name project.name
-            }
-        }
-    }
-
-    publishPlugins.doFirst {
-        assert !kotlin_version.contains('SNAPSHOT')
-    }
-
-    pluginBundle {
-        website = 'https://kotlinlang.org/'
-        vcsUrl = 'https://github.com/JetBrains/kotlin/'
-        description = 'Kotlin plugins for Gradle'
-        tags = ['kotlin']
-
-        mavenCoordinates {
-            groupId = "org.jetbrains.kotlin"
-        }
-    }
-}
\ No newline at end of file
diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/build.gradle b/libraries/tools/kotlin-gradle-plugin-integration-tests/build.gradle
index 296613fd1d6..66b17678301 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/build.gradle
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/build.gradle
@@ -14,10 +14,10 @@ dependencies {
     testCompile project(':kotlin-gradle-subplugin-example')
     testCompile project(':kotlin-allopen')
 
-    testCompile "org.jetbrains.kotlin:annotation-processor-example:$kotlin_version"
+    testCompile project (path: ':examples:annotation-processor-example')
     testCompile "org.jetbrains.kotlin:kotlin-stdlib-jre8:$kotlin_version"
     testCompile "org.jetbrains.kotlin:kotlin-android-extensions:$kotlin_version"
-    testCompile "org.jetbrains.kotlin:kotlin-build-common-test:$kotlin_version"
+    testCompile project (path: ':build-common', configuration: 'tests-jar')
 
     testCompile 'org.jetbrains.kotlin:gradle-api:2.2'
 }
diff --git a/libraries/tools/kotlin-gradle-plugin/build.gradle b/libraries/tools/kotlin-gradle-plugin/build.gradle
index fe713be446f..1b3782453e0 100644
--- a/libraries/tools/kotlin-gradle-plugin/build.gradle
+++ b/libraries/tools/kotlin-gradle-plugin/build.gradle
@@ -43,7 +43,7 @@ dependencies {
     agp25CompileOnly 'org.codehaus.groovy:groovy-all:2.3.9'
     agp25CompileOnly gradleApi()
 
-    testCompile "org.jetbrains.kotlin:kotlin-build-common-test:$kotlin_version"
+    testCompile project (path: ':build-common', configuration: 'tests-jar')
     testCompile "org.jetbrains.kotlin:kotlin-test-junit:$kotlin_version"
     testCompile "junit:junit:4.12"
 }
diff --git a/libraries/tools/kotlin-reflect/build.gradle b/libraries/tools/kotlin-reflect/build.gradle
index 8ffd8564790..db0813e83b2 100644
--- a/libraries/tools/kotlin-reflect/build.gradle
+++ b/libraries/tools/kotlin-reflect/build.gradle
@@ -19,7 +19,7 @@ configureJvmProject(project)
 configurePublishing(project)
 
 
-def core = "${rootDir}/../core"
+def core = "${rootDir}//core"
 def annotationsSrc = "${buildDir}/annotations"
 def relocatedCoreSrc = "${buildDir}/core-relocated"
 
@@ -47,9 +47,10 @@ configurations {
 dependencies {
     proguardDeps project(':kotlin-stdlib')
     shadows 'javax.inject:javax.inject:1'
-    shadows project(path: ':tools:protobuf-lite')
+    shadows project(path: ':custom-dependencies:protobuf-lite', configuration: 'default')
 
     compile project(':kotlin-stdlib')
+    compile project(path: ':custom-dependencies:protobuf-lite', configuration: 'default')
 }
 
 task copyAnnotations(type: Sync) {
@@ -70,6 +71,7 @@ compileJava {
 
 compileKotlin {
     dependsOn copyAnnotations
+    dependsOn ':custom-dependencies:protobuf-lite:prepare'
     kotlinOptions {
         freeCompilerArgs = ["-version",
                             "-Xallow-kotlin-package",
@@ -107,7 +109,7 @@ createScriptTask(project, "stripMetadata") {
     inputs.file(inputJar)
     outputs.file(outputJar)
     args += [
-            "${rootDir}/../generators/infrastructure/strip-kotlin-annotations.kts",
+            "${rootDir}/generators/infrastructure/strip-kotlin-annotations.kts",
             "kotlin/Metadata",
             "kotlin/reflect/jvm/internal/impl/.*",
             inputJar,
@@ -115,7 +117,6 @@ createScriptTask(project, "stripMetadata") {
     ]
 }
 
-
 def mainArchiveName = "${archivesBaseName}-${project.version}.jar"
 def outputJarPath = "${libsDir}/${mainArchiveName}"
 def rtJar = ['jre/lib/rt.jar', '../Classes/classes.jar'].collect { new File(JDK_16, it) }.find { it.isFile() }
diff --git a/libraries/tools/kotlin-stdlib-gen/build.gradle b/libraries/tools/kotlin-stdlib-gen/build.gradle
index 6d5bd2bbf17..e0ca9f660d5 100644
--- a/libraries/tools/kotlin-stdlib-gen/build.gradle
+++ b/libraries/tools/kotlin-stdlib-gen/build.gradle
@@ -5,7 +5,7 @@ sourceSets {
 }
 
 dependencies {
-    compile "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_gradle_plugin_version"
+    compile "org.jetbrains.kotlin:kotlin-stdlib:$kotlin_version"
 }
 
 compileKotlin {
@@ -17,5 +17,5 @@ task run(type: JavaExec) {
     group 'application'
     main 'generators.GenerateStandardLibKt'
     classpath sourceSets.main.runtimeClasspath
-    args = ["${rootDir}/.."]
+    args = ["${rootDir}"]
 }
\ No newline at end of file
diff --git a/libraries/tools/kotlin-stdlib-js-merger/build.gradle b/libraries/tools/kotlin-stdlib-js-merger/build.gradle
index ace09028ed4..d74b0f5d13d 100644
--- a/libraries/tools/kotlin-stdlib-js-merger/build.gradle
+++ b/libraries/tools/kotlin-stdlib-js-merger/build.gradle
@@ -3,7 +3,7 @@ description = 'Merge utility for Kotlin Standard Library for JS'
 apply plugin: 'kotlin'
 
 dependencies {
-    compile files("$distDir/kotlin-compiler-for-maven.jar")
+    compile "org.jetbrains.kotlin:kotlin-compiler:$kotlin_version"
 }
 
 sourceSets {
diff --git a/libraries/tools/runtime/build.gradle b/libraries/tools/runtime/build.gradle
index c59d62f61cb..3332edd3a2d 100644
--- a/libraries/tools/runtime/build.gradle
+++ b/libraries/tools/runtime/build.gradle
@@ -13,8 +13,8 @@ sourceSets {
     if(!System.properties.'idea.active')
     main {
         java {
-            srcDir "${rootDir}/../core/builtins/src"
-            srcDir "${rootDir}/../core/runtime.jvm/src"
+            srcDir "${rootDir}/core/builtins/src"
+            srcDir "${rootDir}/core/runtime.jvm/src"
             exclude 'org/jetbrains/annotations/**'
         }
         kotlin {
@@ -25,13 +25,13 @@ sourceSets {
 
 jar {
     manifestAttributes(manifest, project, 'Main')
-    from("${rootDir}/../dist/builtins")
+    from("${rootDir}/dist/builtins")
 }
 
 sourcesJar {
     classifier = 'sources'
     from sourceSets.main.kotlin
-    from "${rootDir}/../core/builtins/native"
+    from "${rootDir}/core/builtins/native"
 }
 
 artifacts {
@@ -44,7 +44,7 @@ compileKotlin {
         freeCompilerArgs = [
                 "-Xallow-kotlin-package",
                 "-Xdump-declarations-to", "${buildDir}/runtime-declarations.json",
-                "-cp", "${rootDir}/../dist/builtins",
+                "-cp", "${rootDir}/dist/builtins",
                 "-module-name", project.name
         ]
     }
diff --git a/libraries/tools/script-runtime/build.gradle b/libraries/tools/script-runtime/build.gradle
index 6be933774a5..0ff4706d856 100644
--- a/libraries/tools/script-runtime/build.gradle
+++ b/libraries/tools/script-runtime/build.gradle
@@ -12,7 +12,7 @@ dependencies {
 sourceSets {
     main {
         kotlin {
-            srcDir "${rootDir}/../core/script.runtime/src"
+            srcDir "${rootDir}/core/script.runtime/src"
         }
     }
 }