diff --git a/buildSrc/src/main/kotlin/io/spine/dependency/local/Base.kt b/buildSrc/src/main/kotlin/io/spine/dependency/local/Base.kt
index cec4631c..f2f0507d 100644
--- a/buildSrc/src/main/kotlin/io/spine/dependency/local/Base.kt
+++ b/buildSrc/src/main/kotlin/io/spine/dependency/local/Base.kt
@@ -33,8 +33,8 @@ package io.spine.dependency.local
  */
 @Suppress("ConstPropertyName", "unused")
 object Base {
-    const val version = "2.0.0-SNAPSHOT.400"
-    const val versionForBuildScript = "2.0.0-SNAPSHOT.403"
+    const val version = "2.0.0-SNAPSHOT.404"
+    const val versionForBuildScript = "2.0.0-SNAPSHOT.404"
     const val group = Spine.group
     private const val prefix = "spine"
     const val libModule = "$prefix-base"
diff --git a/buildSrc/src/main/kotlin/io/spine/gradle/publish/PublishingExts.kt b/buildSrc/src/main/kotlin/io/spine/gradle/publish/PublishingExts.kt
index 480d3e7b..56221d57 100644
--- a/buildSrc/src/main/kotlin/io/spine/gradle/publish/PublishingExts.kt
+++ b/buildSrc/src/main/kotlin/io/spine/gradle/publish/PublishingExts.kt
@@ -35,6 +35,7 @@ import java.util.*
 import org.gradle.api.InvalidUserDataException
 import org.gradle.api.Project
 import org.gradle.api.Task
+import org.gradle.api.file.DuplicatesStrategy
 import org.gradle.api.publish.PublicationContainer
 import org.gradle.api.publish.PublishingExtension
 import org.gradle.api.publish.maven.MavenPublication
@@ -248,8 +249,16 @@ fun Project.sourcesJar(): TaskProvider<Jar> = tasks.getOrCreate("sourcesJar") {
     description = "Assembles a JAR with Java, Kotlin, and Proto sources from the `main` source set"
     dependOnGenerateProto()
     archiveClassifier.set("sources")
-    from(sourceSets["main"].allSource) // Puts Java and Kotlin sources.
-    from(protoSources()) // Puts Proto sources.
+    // `allSource` also sees the generated `proto-resources` directory, which bundles
+    // copies of `.proto` files (this module's own and its dependencies') as runtime resources.
+    // This behavior starts from Protobuf Gradle Plugin 0.10.0, and it is not expected
+    // to be changed in the future.
+    // This is why we do not call `from(protoSources())` in this function any more.
+    from(sourceSets["main"].allSource)
+
+    // Even if there are duplicates in sources, we want only one.
+    duplicatesStrategy = DuplicatesStrategy.EXCLUDE
+
     exclude("desc.ref", "*.desc") // Exclude descriptor files and the descriptor reference.
 }
 
diff --git a/config b/config
index 8311abe2..f8d5a1dd 160000
--- a/config
+++ b/config
@@ -1 +1 @@
-Subproject commit 8311abe241a65611a1f34ff237a0d02f2ca5ff02
+Subproject commit f8d5a1ddc6aaffca909b644905fcc9b6021e749f
diff --git a/docs/dependencies/dependencies.md b/docs/dependencies/dependencies.md
index 914f18ea..4ff75106 100644
--- a/docs/dependencies/dependencies.md
+++ b/docs/dependencies/dependencies.md
@@ -1,6 +1,6 @@
 
 
-# Dependencies of `io.spine.tools:classic-codegen:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:classic-codegen:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -828,14 +828,14 @@
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:gradle-plugin-api:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:gradle-plugin-api:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -1734,14 +1734,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:gradle-plugin-api-test-fixtures:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:gradle-plugin-api-test-fixtures:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -1776,7 +1776,7 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
      * **Project URL:** [https://github.com/google/gson/gson](https://github.com/google/gson/gson)
      * **License:** [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0.txt)
 
-1.  **Group** : com.google.errorprone. **Name** : error_prone_annotations. **Version** : 2.41.0.
+1.  **Group** : com.google.errorprone. **Name** : error_prone_annotations. **Version** : 2.47.0.
      * **Project URL:** [https://errorprone.info/error_prone_annotations](https://errorprone.info/error_prone_annotations)
      * **License:** [Apache 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
@@ -1784,7 +1784,7 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
      * **Project URL:** [https://github.com/google/guava/](https://github.com/google/guava/)
      * **License:** [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
-1.  **Group** : com.google.guava. **Name** : guava. **Version** : 33.5.0-jre.
+1.  **Group** : com.google.guava. **Name** : guava. **Version** : 33.6.0-jre.
      * **Project URL:** [https://github.com/google/guava](https://github.com/google/guava)
      * **License:** [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
@@ -1918,7 +1918,7 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
      * **Project URL:** [https://github.com/google/gson/gson](https://github.com/google/gson/gson)
      * **License:** [Apache-2.0](https://www.apache.org/licenses/LICENSE-2.0.txt)
 
-1.  **Group** : com.google.errorprone. **Name** : error_prone_annotations. **Version** : 2.41.0.
+1.  **Group** : com.google.errorprone. **Name** : error_prone_annotations. **Version** : 2.47.0.
      * **Project URL:** [https://errorprone.info/error_prone_annotations](https://errorprone.info/error_prone_annotations)
      * **License:** [Apache 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
@@ -1930,7 +1930,7 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
      * **Project URL:** [https://github.com/google/guava/](https://github.com/google/guava/)
      * **License:** [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
-1.  **Group** : com.google.guava. **Name** : guava. **Version** : 33.5.0-jre.
+1.  **Group** : com.google.guava. **Name** : guava. **Version** : 33.6.0-jre.
      * **Project URL:** [https://github.com/google/guava](https://github.com/google/guava)
      * **License:** [Apache License, Version 2.0](http://www.apache.org/licenses/LICENSE-2.0.txt)
 
@@ -2212,14 +2212,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:gradle-root-plugin:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:gradle-root-plugin:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -3070,14 +3070,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:intellij-platform:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:intellij-platform:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : be.cyberelf.nanoxml. **Name** : nanoxml. **Version** : 2.2.3.
@@ -4151,14 +4151,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:46 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:intellij-platform-java:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:intellij-platform-java:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : be.cyberelf.nanoxml. **Name** : nanoxml. **Version** : 2.2.3.
@@ -5930,14 +5930,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:46 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:jvm-tool-plugins:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:jvm-tool-plugins:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -6780,14 +6780,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:jvm-tools:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:jvm-tools:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : org.jetbrains. **Name** : annotations. **Version** : 26.1.0.
@@ -7547,14 +7547,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:plugin-base:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:plugin-base:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -8405,14 +8405,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:plugin-testlib:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:plugin-testlib:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.auto.value. **Name** : auto-value-annotations. **Version** : 1.11.1.
@@ -9367,14 +9367,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:protobuf-setup-plugins:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:protobuf-setup-plugins:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -10237,14 +10237,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:45 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:psi:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:psi:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : be.cyberelf.nanoxml. **Name** : nanoxml. **Version** : 2.2.3.
@@ -11345,14 +11345,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:46 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:psi-java:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:psi-java:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : be.cyberelf.nanoxml. **Name** : nanoxml. **Version** : 2.2.3.
@@ -13167,14 +13167,14 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:46 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
 
 
 
 
-# Dependencies of `io.spine.tools:tool-base:2.0.0-SNAPSHOT.397`
+# Dependencies of `io.spine.tools:tool-base:2.0.0-SNAPSHOT.398`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -14054,6 +14054,6 @@ This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Mon Jun 08 15:00:17 WEST 2026** using 
+This report was generated on **Mon Jun 08 18:51:46 WEST 2026** using 
 [Gradle-License-Report plugin](https://github.com/jk1/Gradle-License-Report) by Evgeny Naumenko, licensed under 
 [Apache 2.0 License](https://github.com/jk1/Gradle-License-Report/blob/master/LICENSE).
\ No newline at end of file
diff --git a/docs/dependencies/pom.xml b/docs/dependencies/pom.xml
index 22b5ce53..371afe2f 100644
--- a/docs/dependencies/pom.xml
+++ b/docs/dependencies/pom.xml
@@ -10,7 +10,7 @@ all modules and does not describe the project structure per-subproject.
  -->
 <groupId>io.spine.tools</groupId>
 <artifactId>tool-base</artifactId>
-<version>2.0.0-SNAPSHOT.397</version>
+<version>2.0.0-SNAPSHOT.398</version>
 
 <inceptionYear>2015</inceptionYear>
 
@@ -170,7 +170,7 @@ all modules and does not describe the project structure per-subproject.
   <dependency>
     <groupId>io.spine</groupId>
     <artifactId>spine-base</artifactId>
-    <version>2.0.0-SNAPSHOT.400</version>
+    <version>2.0.0-SNAPSHOT.404</version>
     <scope>compile</scope>
   </dependency>
   <dependency>
diff --git a/psi-java/src/test/kotlin/io/spine/tools/psi/PsiElementExtsSpec.kt b/psi-java/src/test/kotlin/io/spine/tools/psi/PsiElementExtsSpec.kt
index 0d22624c..6bd8447f 100644
--- a/psi-java/src/test/kotlin/io/spine/tools/psi/PsiElementExtsSpec.kt
+++ b/psi-java/src/test/kotlin/io/spine/tools/psi/PsiElementExtsSpec.kt
@@ -26,7 +26,6 @@
 
 package io.spine.tools.psi
 
-import com.intellij.psi.PsiJavaFile
 import io.kotest.matchers.nulls.shouldNotBeNull
 import io.spine.tools.psi.java.FileSystem
 import io.spine.tools.psi.java.topLevelClass
diff --git a/version.gradle.kts b/version.gradle.kts
index 776291ac..9df04f2c 100644
--- a/version.gradle.kts
+++ b/version.gradle.kts
@@ -24,4 +24,4 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-val versionToPublish: String by extra("2.0.0-SNAPSHOT.397")
+val versionToPublish: String by extra("2.0.0-SNAPSHOT.398")