diff --git a/dokka-runners/cli/build.gradle.kts b/dokka-runners/cli/build.gradle.kts
index 6633dd847f..8a42754246 100644
--- a/dokka-runners/cli/build.gradle.kts
+++ b/dokka-runners/cli/build.gradle.kts
@@ -8,11 +8,15 @@ import org.jetbrains.registerDokkaArtifactPublication
 plugins {
     id("org.jetbrains.conventions.kotlin-jvm")
     id("org.jetbrains.conventions.maven-publish")
-    id("com.github.johnrengelman.shadow")
+
+    // TODO [structure-refactoring] this plugin should not contain the version, it's declared in build-logic
+    // for some reason, it doesn't want to be resolved without the version, even though it works in other subprojects
+    id("com.github.johnrengelman.shadow") version "7.1.2"
 }
 
 dependencies {
-    implementation(projects.core)
+    // TODO [structure-refactoring] the name of the artifact should be `dokka-core`. Add substitution
+    implementation("org.jetbrains.dokka:core")
     implementation(libs.kotlinx.cli)
 
     testImplementation(kotlin("test"))
diff --git a/dokka-runners/cli/settings.gradle.kts b/dokka-runners/cli/settings.gradle.kts
index 82842a6923..ebb9606611 100644
--- a/dokka-runners/cli/settings.gradle.kts
+++ b/dokka-runners/cli/settings.gradle.kts
@@ -18,6 +18,7 @@ pluginManagement {
 dependencyResolutionManagement {
     repositories {
         mavenCentral()
+        google()
     }
 
     versionCatalogs {
@@ -28,3 +29,5 @@ dependencyResolutionManagement {
 }
 
 enableFeaturePreview("TYPESAFE_PROJECT_ACCESSORS")
+
+includeBuild("../../dokka-subprojects")
diff --git a/dokka-runners/gradle-plugin-classic/build.gradle.kts b/dokka-runners/gradle-plugin-classic/build.gradle.kts
index fd3197adb5..a9a766dfc2 100644
--- a/dokka-runners/gradle-plugin-classic/build.gradle.kts
+++ b/dokka-runners/gradle-plugin-classic/build.gradle.kts
@@ -9,8 +9,7 @@ plugins {
 }
 
 dependencies {
-    // TODO dependency should be `org.jetbrains.dokka:dokka-core`, because that's the published artifact ID, but the
-    //      core subproject name doesn't match this
+    // TODO [structure-refactoring] the name of the artifact should be `dokka-core`. Add substitution
     api("org.jetbrains.dokka:core")
 
     compileOnly(libs.gradlePlugin.kotlin)
diff --git a/dokka-runners/maven-plugin/build.gradle.kts b/dokka-runners/maven-plugin/build.gradle.kts
index 825493ad27..0c53b51dc8 100644
--- a/dokka-runners/maven-plugin/build.gradle.kts
+++ b/dokka-runners/maven-plugin/build.gradle.kts
@@ -11,7 +11,8 @@ plugins {
 }
 
 dependencies {
-    implementation(projects.core)
+    // TODO [structure-refactoring] the name of the artifact should be `dokka-core`. Add substitution
+    implementation("org.jetbrains.dokka:core")
 
     implementation(libs.apacheMaven.core)
     implementation(libs.apacheMaven.pluginApi)
diff --git a/settings.gradle.kts b/settings.gradle.kts
index 108a35ead8..3d79294f8b 100644
--- a/settings.gradle.kts
+++ b/settings.gradle.kts
@@ -58,60 +58,16 @@ plugins {
     `gradle-enterprise`
 }
 
-includeBuild("dokka-integration-tests")
+// TODO [structure-refactoring] enable all
+//includeBuild("dokka-integration-tests")
 includeBuild("dokka-subprojects")
-includeBuild("dokka-runners/gradle-plugin")
+//includeBuild("dokka-runners/gradle-plugin")
 includeBuild("dokka-runners/gradle-plugin-classic")
 includeBuild("dokka-runners/maven-plugin")
 includeBuild("dokka-runners/cli")
 
-include(
-//    ":core",
-//    ":core:test-api",
-//    ":core:content-matcher-test-utils",
-//
-//    ":subprojects",
-//
-//    ":subprojects:analysis-java-psi",
-//    ":subprojects:analysis-kotlin-api",
-//    ":subprojects:analysis-kotlin-descriptors",
-//    ":subprojects:analysis-kotlin-descriptors:compiler",
-//    ":subprojects:analysis-kotlin-descriptors:ide",
-//    ":subprojects:analysis-kotlin-symbols",
-//    ":subprojects:analysis-markdown-jb",
-//
-////    ":runners:gradle-plugin",
-////    ":runners:cli",
-////    ":runners:maven-plugin",
-//
-//    ":plugins:base",
-//    ":plugins:base:frontend",
-//    ":plugins:base:base-test-utils",
-//    ":plugins:all-modules-page",
-//    ":plugins:templating",
-//    ":plugins:versioning",
-//    ":plugins:android-documentation",
-//
-//    ":plugins:mathjax",
-//    ":plugins:gfm",
-//    ":plugins:gfm:gfm-template-processing",
-//    ":plugins:jekyll",
-//    ":plugins:jekyll:jekyll-template-processing",
-//    ":plugins:kotlin-as-java",
-//    ":plugins:javadoc",
-//
-////    ":integration-tests",
-////    ":integration-tests:gradle",
-////    ":integration-tests:cli",
-////    ":integration-tests:maven",
-//
-//    ":docs-developer",
-)
-
 val isCiBuild = System.getenv("GITHUB_ACTIONS") != null || System.getenv("TEAMCITY_VERSION") != null
 
-
-
 gradleEnterprise {
     buildScan {
         termsOfServiceUrl = "https://gradle.com/terms-of-service"
@@ -119,6 +75,4 @@ gradleEnterprise {
         publishAlwaysIf(isCiBuild)
     }
 }
-
-
 enableFeaturePreview("TYPESAFE_PROJECT_ACCESSORS")