diff --git a/.agents/tasks/fix-test-source-set-duplicates.md b/.agents/tasks/fix-test-source-set-duplicates.md
new file mode 100644
index 0000000000..d65b11964a
--- /dev/null
+++ b/.agents/tasks/fix-test-source-set-duplicates.md
@@ -0,0 +1,54 @@
+---
+slug: fix-test-source-set-duplicates
+branch: claude/vibrant-jang-fa76b9
+owner: claude
+status: in-review
+started: 2026-06-30
+---
+
+## Goal
+
+Fix [issue #19](https://github.com/SpineEventEngine/compiler/issues/19):
+generated source sets in tests may contain duplicates. The Compiler reads the
+`protoc` output and writes processed code into a separate directory; both must
+not reach the Java/Kotlin compiler at once, or compilation fails with
+`duplicate class` errors. This "sometimes does not work for the test source
+set."
+
+## Context
+
+- `protoc` writes to `build/generated/sources/proto/<sourceSet>/{java,kotlin}`;
+  the Compiler writes to `generated/<sourceSet>/{java,kotlin}`.
+- Deduplication lived in `configureCompileTasks` (live compile-task filtering) in
+  ProtoData until a 2023 commit ("Improve filtering of duplicated generated
+  sources") replaced it with an eager, one-time source-set rewrite, now in
+  tool-base's `GeneratedSourcePlugin.configureSourceSetDirs`.
+- The eager rewrite is fragile: plugin-application order, a symlinked project
+  path (the old `residesIn` compared a canonical path to a merely absolute one),
+  or a consumer plugin re-adding the directory can leave the `protoc` output in
+  the source set.
+
+## Plan
+
+- [x] Reproduce: `test-source-set` fixture with protos in `main` + `test`; an
+      `afterEvaluate` re-adds the `protoc` output dir to the `test` source set,
+      reproducing the leaked state. Confirmed `compileTestJava` fails with
+      `duplicate class`.
+- [x] Fix (compiler-side, order-independent): re-introduce live compile-task
+      filtering in `Plugin.excludeProtocOutputFromCompilation()` — re-set
+      `JavaCompile.source` to a filtered view and add an `exclude` spec to
+      `KotlinCompile`. Skips the deprecated in-place mode.
+- [x] Harden `Paths.residesIn` to canonicalize both operands (symlink-safe).
+- [x] Regression test `keep duplicate generated classes out of the 'test'
+      compilation` asserts `testClasses` succeeds.
+- [x] Version bump `2.0.0-SNAPSHOT.057` → `.058`.
+- [x] Full `PluginSpec` green: 16 tests, 0 failures (1 pre-existing skip).
+      `:gradle-plugin:detekt` (the `check` gate) passes.
+
+## Log
+- 2026-06-30 — reproduced RED (duplicate class in `compileTestJava`), implemented
+  the fix, verified GREEN with a marker proving the fixed plugin code executed in
+  the inner testkit build.
+- Note: local incremental/build-cache is stale in this checkout; verifying
+  functional tests needs `--rerun-tasks --no-build-cache` and `arch -arm64`
+  (gradle-doctor Rosetta check). See auto-memory `gradle-arch-arm64`.
diff --git a/build.gradle.kts b/build.gradle.kts
index 920bd99ed9..fdd006043f 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -128,7 +128,7 @@ KoverConfig.applyTo(project)
  * publishing in the root project.
  */
 val projectsToPublish: Set<String> = the<SpinePublishing>().modules
-val localPublish by tasks.registering {
+val localPublish = tasks.register("localPublish") {
     /*
        Integration tests need the plugin subproject published to Maven Local too
        because they apply the plugin.
@@ -187,7 +187,7 @@ fun materializeTestsLink(linkName: String) {
  * This build should run _only_ if all tests of all modules passed.
  * Otherwise, integration tests make little sense.
  */
-val integrationTest by tasks.registering(RunBuild::class) {
+val integrationTest = tasks.register<RunBuild>("integrationTest") {
     directory = "$rootDir/tests"
     /* The `tests` build consumes the Compiler published to Maven Local by `localPublish`,
        so the build cache in that build exercises the plugin under development. */
@@ -195,7 +195,7 @@ val integrationTest by tasks.registering(RunBuild::class) {
     dependsOn(localPublish)
     subprojects.forEach {
         it.tasks.findByName("test")?.let { testTask ->
-            this@registering.dependsOn(testTask)
+            this@register.dependsOn(testTask)
         }
     }
     doFirst {
diff --git a/buildSrc/src/main/kotlin/io/spine/gradle/fs/LazyTempPath.kt b/buildSrc/src/main/kotlin/io/spine/gradle/fs/LazyTempPath.kt
index 0344819f22..b31cd3087f 100644
--- a/buildSrc/src/main/kotlin/io/spine/gradle/fs/LazyTempPath.kt
+++ b/buildSrc/src/main/kotlin/io/spine/gradle/fs/LazyTempPath.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright 2025, TeamDev. All rights reserved.
+ * Copyright 2026, TeamDev. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -41,11 +41,16 @@ import java.nio.file.WatchService
  *
  * After the first usage, the instances of this type delegate all calls to the internally
  * created instance of [Path] created with [createTempDirectory].
+ *
+ * The directory is created under the [shared base directory][SpineTempDir], which is removed
+ * when the JVM — the Gradle daemon — shuts down. Build tasks delete their own directories
+ * eagerly as the primary cleanup; this shutdown removal is a safety net, so a directory does
+ * not outlive the daemon even when a build fails before its eager cleanup runs.
  */
 @Suppress("TooManyFunctions")
 class LazyTempPath(private val prefix: String) : Path {
 
-    private val delegate: Path by lazy { createTempDirectory(prefix) }
+    private val delegate: Path by lazy { createTempDirectory(SpineTempDir.path, prefix) }
 
     override fun compareTo(other: Path): Int = delegate.compareTo(other)
 
diff --git a/buildSrc/src/main/kotlin/io/spine/gradle/fs/SpineTempDir.kt b/buildSrc/src/main/kotlin/io/spine/gradle/fs/SpineTempDir.kt
new file mode 100644
index 0000000000..d6e856e01f
--- /dev/null
+++ b/buildSrc/src/main/kotlin/io/spine/gradle/fs/SpineTempDir.kt
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2026, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package io.spine.gradle.fs
+
+import java.nio.file.Files.createDirectories
+import java.nio.file.Files.createTempDirectory
+import java.nio.file.Path
+
+/**
+ * A per-JVM parent directory for the temporary directories created by the build.
+ *
+ * The directory is created [lazily][path] under a common, attributable namespace —
+ * `<java.io.tmpdir>/io.spine.gradle.fs`, named after the package of [LazyTempPath] — so
+ * that leftover files are easy to attribute. Within that namespace, each JVM gets its own
+ * subdirectory named after the process id, so concurrent Gradle daemons never delete one
+ * another's temporary files.
+ *
+ * Upon creation, the per-JVM directory is scheduled for recursive removal when the JVM
+ * shuts down. This is a safety net should the explicit cleanup performed by the build
+ * tasks not run — for example, when a build fails before reaching it. The shared namespace
+ * directory itself is intentionally left in place: deleting it on shutdown could wipe
+ * directories still in use by another JVM running on the same machine.
+ *
+ * @see LazyTempPath
+ */
+internal object SpineTempDir {
+
+    /**
+     * The per-JVM directory, created on the first access and removed on JVM shutdown.
+     */
+    val path: Path by lazy { createPerJvmDir() }
+
+    private fun createPerJvmDir(): Path {
+        val namespace = Path.of(systemTempDir(), LazyTempPath::class.java.packageName)
+        createDirectories(namespace)
+        // A per-JVM directory keeps concurrent Gradle daemons from deleting one another's
+        // files when their shutdown hooks fire. The PID makes a leftover directory easy
+        // to attribute; `createTempDirectory` adds a random suffix so that a reused PID
+        // still yields a unique directory.
+        val pid = ProcessHandle.current().pid()
+        val jvmDir = createTempDirectory(namespace, "$pid-")
+        deleteRecursivelyOnShutdown(jvmDir)
+        return jvmDir
+    }
+
+    /**
+     * Obtains the value of the system property pointing to the temporary directory.
+     */
+    private fun systemTempDir(): String =
+        checkNotNull(System.getProperty("java.io.tmpdir")) {
+            "The `java.io.tmpdir` system property is not set."
+        }
+
+    /**
+     * Requests the recursive removal of the given [directory] when the JVM shuts down.
+     *
+     * @see Runtime.addShutdownHook
+     */
+    private fun deleteRecursivelyOnShutdown(directory: Path) {
+        val runtime = Runtime.getRuntime()
+        runtime.addShutdownHook(Thread {
+            val deleted = directory.toFile().deleteRecursively()
+            if (!deleted) {
+                System.err.println("Unable to delete the temporary directory `$directory`.")
+            }
+        })
+    }
+}
diff --git a/buildSrc/src/test/kotlin/io/spine/gradle/fs/LazyTempPathSpec.kt b/buildSrc/src/test/kotlin/io/spine/gradle/fs/LazyTempPathSpec.kt
new file mode 100644
index 0000000000..260e852fe2
--- /dev/null
+++ b/buildSrc/src/test/kotlin/io/spine/gradle/fs/LazyTempPathSpec.kt
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2026, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package io.spine.gradle.fs
+
+import io.kotest.matchers.shouldBe
+import io.kotest.matchers.string.shouldContain
+import org.junit.jupiter.api.DisplayName
+import org.junit.jupiter.api.Test
+
+@DisplayName("`LazyTempPath` should")
+class LazyTempPathSpec {
+
+    @Test
+    fun `create the directory on the first use`() {
+        val directory = LazyTempPath("created").toFile()
+
+        directory.exists() shouldBe true
+        directory.isDirectory shouldBe true
+    }
+
+    @Test
+    fun `create the directory under the system temporary directory`() {
+        val path = LazyTempPath("under-tmp").toString()
+
+        path shouldContain systemTempDir()
+    }
+
+    @Test
+    fun `create the directory under a folder named after its package`() {
+        val path = LazyTempPath("under-base").toString()
+
+        path shouldContain LazyTempPath::class.java.packageName
+    }
+
+    @Test
+    fun `place all instances under the same base directory`() {
+        val first = LazyTempPath("first").toFile()
+        val second = LazyTempPath("second").toFile()
+
+        first.parentFile shouldBe second.parentFile
+        first.parentFile.toString() shouldBe SpineTempDir.path.toString()
+    }
+}
+
+private fun systemTempDir(): String = System.getProperty("java.io.tmpdir")
diff --git a/buildSrc/src/main/kotlin/version-to-resources.gradle.kts b/buildSrc/src/test/kotlin/io/spine/gradle/fs/SpineTempDirSpec.kt
similarity index 61%
rename from buildSrc/src/main/kotlin/version-to-resources.gradle.kts
rename to buildSrc/src/test/kotlin/io/spine/gradle/fs/SpineTempDirSpec.kt
index 6ac408c574..8bf42500a8 100644
--- a/buildSrc/src/main/kotlin/version-to-resources.gradle.kts
+++ b/buildSrc/src/test/kotlin/io/spine/gradle/fs/SpineTempDirSpec.kt
@@ -1,5 +1,5 @@
 /*
- * Copyright 2025, TeamDev. All rights reserved.
+ * Copyright 2026, TeamDev. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -24,36 +24,31 @@
  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  */
 
-plugins {
-    java
-}
+package io.spine.gradle.fs
 
-val versionDir = layout.buildDirectory.dir("version").get().asFile.path
+import io.kotest.matchers.shouldBe
+import java.nio.file.Path
+import org.junit.jupiter.api.DisplayName
+import org.junit.jupiter.api.Test
 
-/**
- * This file, containing the version of ProtoData, is generated at build time and included into
- * the project's resources.
- *
- * Please search for the usages of "version.txt" when making changes.
- */
-val versionFile = "$versionDir/version.txt"
+@DisplayName("`SpineTempDir` should")
+class SpineTempDirSpec {
 
-sourceSets {
-    main {
-        resources.srcDir(versionDir)
-    }
-}
+    @Test
+    fun `place its per-JVM directory under the package-named namespace`() {
+        val namespace = Path.of(
+            System.getProperty("java.io.tmpdir"),
+            LazyTempPath::class.java.packageName
+        )
 
-val createVersionFile by tasks.registering {
+        SpineTempDir.path.parent shouldBe namespace
+    }
 
-    inputs.property("version", project.version)
-    outputs.file(versionFile)
+    @Test
+    fun `create the directory on access`() {
+        val directory = SpineTempDir.path.toFile()
 
-    doLast {
-        file(versionFile).writeText(project.version.toString())
+        directory.exists() shouldBe true
+        directory.isDirectory shouldBe true
     }
 }
-
-tasks.processResources {
-    dependsOn(createVersionFile)
-}
diff --git a/cli/build.gradle.kts b/cli/build.gradle.kts
index 3e15e65aa2..207c1056eb 100644
--- a/cli/build.gradle.kts
+++ b/cli/build.gradle.kts
@@ -36,7 +36,6 @@ import io.spine.gradle.publish.setup
 plugins {
     module
     application
-    `version-to-resources`
     `write-manifest`
     `build-proto-model`
     `maven-publish`
diff --git a/config b/config
index fdf78d7a2c..73d246ad7e 160000
--- a/config
+++ b/config
@@ -1 +1 @@
-Subproject commit fdf78d7a2c2372cead94ea29e9155707e200b94e
+Subproject commit 73d246ad7ebe4e3b8e3f0c14335152435daa1b20
diff --git a/docs/dependencies/dependencies.md b/docs/dependencies/dependencies.md
index eda7690486..8726f5f5e8 100644
--- a/docs/dependencies/dependencies.md
+++ b/docs/dependencies/dependencies.md
@@ -1,6 +1,6 @@
 
 
-# Dependencies of `io.spine.tools:compiler-api:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-api:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -1099,14 +1099,14 @@
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-api-tests:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-api-tests:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 ## Compile, tests, and tooling
@@ -1476,14 +1476,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:16 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:compiler-backend:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-backend:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -2586,14 +2586,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-cli:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-cli:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -3855,14 +3855,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-gradle-api:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-gradle-api:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -4879,14 +4879,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-gradle-plugin:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-gradle-plugin:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -5947,14 +5947,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-jvm:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-jvm:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -7074,14 +7074,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-params:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-params:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -8172,14 +8172,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-protoc-plugin:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-protoc-plugin:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.google.code.findbugs. **Name** : jsr305. **Version** : 3.0.2.
@@ -9012,14 +9012,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-test-env:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-test-env:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -10118,14 +10118,14 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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:compiler-testlib:2.0.0-SNAPSHOT.058`
+# Dependencies of `io.spine.tools:compiler-testlib:2.0.0-SNAPSHOT.059`
 
 ## Runtime
 1.  **Group** : com.fasterxml.jackson. **Name** : jackson-bom. **Version** : 2.22.0.
@@ -11331,6 +11331,6 @@ This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using
 
 The dependencies distributed under several licenses, are used according their commercial-use-friendly license.
 
-This report was generated on **Tue Jun 30 23:13:38 WEST 2026** using 
+This report was generated on **Wed Jul 01 16:19:17 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 93d68f4c7b..b2e383144b 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>compiler</artifactId>
-<version>2.0.0-SNAPSHOT.058</version>
+<version>2.0.0-SNAPSHOT.059</version>
 
 <inceptionYear>2015</inceptionYear>
 
diff --git a/gradle-plugin/build.gradle.kts b/gradle-plugin/build.gradle.kts
index c6cb5f80b1..d5583ad6a8 100644
--- a/gradle-plugin/build.gradle.kts
+++ b/gradle-plugin/build.gradle.kts
@@ -1,5 +1,5 @@
 /*
- * Copyright 2025, TeamDev. All rights reserved.
+ * Copyright 2026, TeamDev. All rights reserved.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -41,7 +41,6 @@ plugins {
     `java-gradle-plugin`
     `maven-publish`
     id("com.gradle.plugin-publish").version("1.3.1")
-    `version-to-resources`
     `write-manifest`
 }
 
@@ -69,13 +68,10 @@ artifactMeta {
     }
 }
 
-@Suppress(
-    "UnstableApiUsage" /* testing suites feature */,
-    "unused" /* suite variable names obtained via `by` calls. */
-)
+@Suppress("UnstableApiUsage") /* testing suites feature */
 testing {
     suites {
-        val test by getting(JvmTestSuite::class) {
+        getByName<JvmTestSuite>("test") {
             useJUnitJupiter(JUnit.version)
             dependencies {
                 implementation(Kotlin.GradlePlugin.lib)
@@ -86,7 +82,7 @@ testing {
             }
         }
 
-        val functionalTest by registering(JvmTestSuite::class) {
+        register<JvmTestSuite>("functionalTest") {
             useJUnitJupiter(JUnit.version)
             dependencies {
                 implementation(Kotlin.GradlePlugin.lib)
@@ -124,8 +120,7 @@ dependencies {
  * Make functional tests depend on publishing all the submodules to Maven Local so that
  * the Gradle plugin can get all the dependencies when it's applied to the test projects.
  */
-@Suppress("unused")
-val functionalTest: Task by tasks.getting {
+tasks.getByName("functionalTest") {
     val task = this
     productionModules.forEach { subproject ->
         task.dependsOn(":${subproject.name}:publishToMavenLocal")
@@ -137,15 +132,14 @@ java {
     withJavadocJar()
 }
 
-val compilerVersion: String by extra
+val compilerVersion = extra["compilerVersion"] as String
 val isSnapshot = compilerVersion.isSnapshot()
 
-val publishPlugins: Task by tasks.getting {
+val publishPlugins: Task = tasks.getByName("publishPlugins") {
     enabled = !isSnapshot
 }
 
-@Suppress("unused")
-val publish: Task by tasks.getting {
+tasks.getByName("publish") {
     if (!isSnapshot) {
         dependsOn(publishPlugins)
     }
@@ -179,13 +173,12 @@ gradlePlugin {
             tags.set(listOf("spine", "ddd", "protobuf", "compiler", "code-generation", "codegen"))
         }
     }
-    val functionalTest by sourceSets.getting
+    val functionalTest = sourceSets.getByName("functionalTest")
     testSourceSets(
         functionalTest
     )
 }
 
-
 tasks {
     check {
         dependsOn(testing.suites.named("functionalTest"))
diff --git a/gradle-plugin/src/functionalTest/kotlin/io/spine/tools/compiler/gradle/plugin/PluginSpec.kt b/gradle-plugin/src/functionalTest/kotlin/io/spine/tools/compiler/gradle/plugin/PluginSpec.kt
index 9caee83331..0d31200598 100644
--- a/gradle-plugin/src/functionalTest/kotlin/io/spine/tools/compiler/gradle/plugin/PluginSpec.kt
+++ b/gradle-plugin/src/functionalTest/kotlin/io/spine/tools/compiler/gradle/plugin/PluginSpec.kt
@@ -119,6 +119,34 @@ class PluginSpec {
         createProject("java-kotlin-test")
     }
 
+    /**
+     * Verifies that the `test` source set compiles even when the `protoc` output
+     * directory ends up among its source directories.
+     *
+     * The Compiler reads the `protoc` output and writes the processed code into
+     * a separate directory, which is added to the source set. The plugin keeps the
+     * `protoc` output directory out of the compilation so that each generated class
+     * is compiled once. That filtering must hold for the `test` source set too —
+     * see [issue #19](https://github.com/SpineEventEngine/compiler/issues/19).
+     *
+     * The `test-source-set` project re-adds the `protoc` output directory to the
+     * `test` source set after the plugin has configured it, reproducing the state
+     * in which the directory leaked back in. Without the compilation-level filter
+     * the `test` sources contain each generated class twice, and the compilation
+     * fails with duplicate class errors.
+     */
+    @Test
+    fun `keep duplicate generated classes out of the 'test' compilation`() {
+        createProject("test-source-set")
+        val testClasses = TaskName.of("testClasses")
+
+        val result = project.executeTask(testClasses)
+
+        result[CompilerTaskName(SourceSetName.test)] shouldBe SUCCESS
+        result[TaskName.of("compileTestJava")] shouldBe SUCCESS
+        result[TaskName.of("compileTestKotlin")] shouldBe SUCCESS
+    }
+
     private fun launchAndExpectResult(expected: TaskOutcome) {
         val result = launch()
 
diff --git a/gradle-plugin/src/functionalTest/resources/test-source-set/build.gradle.kts b/gradle-plugin/src/functionalTest/resources/test-source-set/build.gradle.kts
new file mode 100644
index 0000000000..268c92ce6d
--- /dev/null
+++ b/gradle-plugin/src/functionalTest/resources/test-source-set/build.gradle.kts
@@ -0,0 +1,94 @@
+/*
+ * Copyright 2026, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+import com.google.protobuf.gradle.ProtobufExtension
+import io.spine.dependency.lib.Protobuf
+import io.spine.gradle.repo.standardToSpineSdk
+import org.gradle.api.tasks.SourceSetContainer
+
+buildscript {
+    standardSpineSdkRepositories()
+}
+
+group = "io.spine.tools.test"
+version = "1.0.0-SNAPSHOT"
+
+plugins {
+    java
+    kotlin("jvm")
+    id("com.google.protobuf")
+    id("@COMPILER_PLUGIN_ID@") version "@COMPILER_VERSION@"
+}
+
+repositories {
+    mavenLocal() // Must come first for `compiler-test-env`.
+    standardToSpineSdk()
+}
+
+spine {
+    compiler {
+        plugins(
+            "io.spine.tools.compiler.test.NoOpRendererPlugin",
+            "io.spine.tools.compiler.test.TestPlugin"
+        )
+    }
+}
+configurations.all {
+    resolutionStrategy {
+        force(
+            io.spine.dependency.local.Base.lib,
+        )
+    }
+}
+
+dependencies {
+    spineCompiler("io.spine.tools:compiler-test-env:+")
+    Protobuf.libs.forEach { implementation(it) }
+}
+
+// Simulate the `protoc` output directory leaking back into the `test` source set.
+//
+// The Compiler reads the `protoc` output from `build/generated/sources/proto/test`
+// and writes its own output under `generated/test`. The plugin removes the
+// `protoc` directories from the source sets to avoid compiling the same class
+// twice. That removal is a one-time rewrite of the source-set directories and is
+// fragile: depending on the plugin-configuration order, a symlinked project path,
+// or a consumer plugin re-adding the directory, the `protoc` output may end up in
+// the `test` source set anyway. We reproduce that final state directly by
+// re-adding the directory after the plugin has configured the source set.
+//
+// Without compile-task-level filtering, `compileTestJava` and `compileTestKotlin`
+// then see each generated class twice and fail with "duplicate class" errors.
+afterEvaluate {
+    val sourceSets = project.extensions.getByType(SourceSetContainer::class.java)
+    val test = sourceSets.getByName("test")
+    // The `protoc` output base directory of the Protobuf Gradle Plugin
+    // (`build/generated/sources/proto` by default).
+    val protocBaseDir = project.extensions.getByType(ProtobufExtension::class.java)
+        .generatedFilesBaseDir
+    test.java.srcDir("$protocBaseDir/test/java")
+    test.java.srcDir("$protocBaseDir/test/kotlin")
+}
diff --git a/gradle-plugin/src/functionalTest/resources/test-source-set/settings.gradle.kts b/gradle-plugin/src/functionalTest/resources/test-source-set/settings.gradle.kts
new file mode 100644
index 0000000000..f5ecc1b72b
--- /dev/null
+++ b/gradle-plugin/src/functionalTest/resources/test-source-set/settings.gradle.kts
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2022, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+pluginManagement {
+    repositories {
+        mavenLocal()
+    }
+}
diff --git a/gradle-plugin/src/functionalTest/resources/test-source-set/src/main/proto/main_scope.proto b/gradle-plugin/src/functionalTest/resources/test-source-set/src/main/proto/main_scope.proto
new file mode 100644
index 0000000000..9ed9c60dd6
--- /dev/null
+++ b/gradle-plugin/src/functionalTest/resources/test-source-set/src/main/proto/main_scope.proto
@@ -0,0 +1,11 @@
+syntax = "proto3";
+
+package spine.compiler.test;
+
+option java_package = "io.spine.tools.compiler.test";
+option java_outer_classname = "MainScopeProto";
+option java_multiple_files = true;
+
+// A `main`-scope definition so that the `main` source set has generated code too.
+message MainScoped {
+}
diff --git a/gradle-plugin/src/functionalTest/resources/test-source-set/src/test/proto/test_scope.proto b/gradle-plugin/src/functionalTest/resources/test-source-set/src/test/proto/test_scope.proto
new file mode 100644
index 0000000000..38ba072050
--- /dev/null
+++ b/gradle-plugin/src/functionalTest/resources/test-source-set/src/test/proto/test_scope.proto
@@ -0,0 +1,14 @@
+syntax = "proto3";
+
+package spine.compiler.test;
+
+option java_package = "io.spine.tools.compiler.test";
+option java_outer_classname = "TestScopeProto";
+option java_multiple_files = true;
+
+// A `test`-scope definition. The Compiler generates code for it under
+// `generated/test`, while `protoc` puts its output under
+// `build/generated/sources/proto/test`. Both must not end up in the `test`
+// source set at the same time, or the compilation fails with duplicate classes.
+message TestScoped {
+}
diff --git a/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Paths.kt b/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Paths.kt
index 431e3a7d92..e4a917481f 100644
--- a/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Paths.kt
+++ b/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Paths.kt
@@ -55,6 +55,27 @@ internal fun Iterable<File>.excluding(excludeDir: File): Set<File> =
 
 /**
  * Tells if this file resides in the given [directory].
+ *
+ * Both paths are resolved to their canonical form before the comparison, so the
+ * check is not defeated by symbolic links. Comparing a canonical path against
+ * a merely absolute one (which keeps symlinks unresolved) could otherwise yield
+ * a false negative when the project resides under a symlinked path — leaving the
+ * `protoc` output directory unfiltered and the generated classes duplicated.
+ *
+ * The comparison is performed on [Path] name components, so a sibling directory
+ * such as `…/test2` is not mistaken for residing in `…/test`.
  */
 internal fun File.residesIn(directory: File): Boolean =
-    canonicalFile.startsWith(directory.absolutePath)
+    residesIn(directory.canonicalFile.toPath())
+
+/**
+ * Tells if this file resides under [canonicalDir] — a path that is *already* in
+ * canonical form.
+ *
+ * Resolving a path to its canonical form is a filesystem operation. This overload
+ * lets a caller canonicalize the directory once and reuse the result across many
+ * files — for example, while filtering a large source set — instead of
+ * re-canonicalizing the directory on every call, as the `File`-typed overload does.
+ */
+internal fun File.residesIn(canonicalDir: Path): Boolean =
+    canonicalFile.toPath().startsWith(canonicalDir)
diff --git a/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Plugin.kt b/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Plugin.kt
index 86882879ac..7cbefd5787 100644
--- a/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Plugin.kt
+++ b/gradle-plugin/src/main/kotlin/io/spine/tools/compiler/gradle/plugin/Plugin.kt
@@ -56,6 +56,7 @@ import io.spine.tools.compiler.params.WorkingDirectory
 import io.spine.tools.gradle.lib.LibraryPlugin
 import io.spine.tools.gradle.lib.spineExtension
 import io.spine.tools.gradle.project.hasJavaOrKotlin
+import io.spine.tools.gradle.project.hasKotlin
 import io.spine.tools.gradle.project.sourceSets
 import io.spine.tools.gradle.task.SpineTaskGroup
 import io.spine.tools.meta.ArtifactMeta
@@ -67,11 +68,16 @@ import io.spine.tools.protobuf.gradle.protobufExtension
 import java.io.File
 import java.nio.file.Path
 import org.gradle.api.Project
+import org.gradle.api.file.FileTreeElement
+import org.gradle.api.specs.Spec
 import org.gradle.api.tasks.Delete
 import org.gradle.api.tasks.SourceSet
 import org.gradle.api.tasks.TaskProvider
+import org.gradle.api.tasks.compile.JavaCompile
+import org.gradle.api.tasks.util.PatternFilterable
 import org.gradle.kotlin.dsl.exclude
 import org.gradle.kotlin.dsl.register
+import org.jetbrains.kotlin.gradle.tasks.KotlinCompilationTask
 
 /**
  * The Gradle plugin of the Spine Compiler.
@@ -299,6 +305,74 @@ private fun Project.configureWithProtobufPlugin(compilerVersion: String) {
         }
         setProtocPluginArtifact(protocPlugin)
         configureGenerateProtoTasks()
+        excludeProtocOutputFromCompilation()
+    }
+}
+
+/**
+ * Excludes the `protoc` output directory from the input of the Java and Kotlin
+ * compilation tasks of this project.
+ *
+ * The Compiler takes the code generated by `protoc` as its input and writes the
+ * processed code into a separate directory (`generated` by default). The plugin
+ * adds that directory to the source sets. The `protoc` output directory
+ * ([protocOutputDir]) must be kept out of the compilation: otherwise each
+ * generated class is compiled twice — once from the `protoc` output and once
+ * from the Compiler output — and the build fails with duplicate class errors.
+ *
+ * The plugin already removes the `protoc` directories from the source sets via
+ * [configureSourceSetDirs][io.spine.tools.protobuf.gradle.plugin.configureSourceSetDirs].
+ * That removal rewrites the source-set directories once during configuration and
+ * does not always hold for the `test` source set: depending on the order in which
+ * the plugins are applied, a symlinked project path, or another plugin re-adding
+ * the directory, the `protoc` output may end up back in the source set. This
+ * function adds an order-independent line of defence by filtering the compilation
+ * input directly. The filter is evaluated when a compilation task resolves its
+ * sources, so it holds regardless of when the directory was added to the source
+ * set.
+ *
+ * The deprecated in-place mode, in which the Compiler overwrites the `protoc`
+ * output instead of writing to a separate directory, is left untouched: there the
+ * generated code legitimately resides in the `protoc` output directory, so
+ * filtering it out would drop it from compilation.
+ *
+ * @see [GenerateProtoTask.configureSourceSetDirs]
+ */
+private fun Project.excludeProtocOutputFromCompilation() {
+    afterEvaluate {
+        // Canonicalize the `protoc` output directory once and reuse it while
+        // filtering each source file, instead of re-canonicalizing it per file.
+        val protocOutput = protocOutputDir.canonicalFile.toPath()
+        val compilerWritesInPlace = generatedDir.toFile().residesIn(protocOutput)
+        if (compilerWritesInPlace) {
+            return@afterEvaluate
+        }
+        // `JavaCompile` ignores an `exclude(Spec)` predicate for the files it
+        // passes to `javac`, so its source is re-set to a filtered view of
+        // itself. The view wraps the task's own (live) source and preserves the
+        // task dependencies it carries, so the generated code is still produced
+        // before compilation.
+        tasks.withType(JavaCompile::class.java).configureEach { task ->
+            task.source = task.source.filter { file ->
+                !file.residesIn(protocOutput)
+            }.asFileTree
+        }
+        // `KotlinCompile` honors `exclude(Spec)` — a live predicate that needs no
+        // source re-wiring. The cast targets `KotlinCompile` (which is a
+        // `PatternFilterable`); any other `KotlinCompilationTask` is skipped.
+        //
+        // The Kotlin Gradle Plugin is a `compileOnly` dependency, so its task type
+        // is not on the runtime classpath. The reference to `KotlinCompilationTask`
+        // is therefore guarded by `hasKotlin()` (a name-based check), keeping the
+        // plugin loadable for consumers that apply it without Kotlin.
+        if (hasKotlin()) {
+            val underProtocOutput = Spec<FileTreeElement> { element ->
+                element.file.residesIn(protocOutput)
+            }
+            tasks.withType(KotlinCompilationTask::class.java).configureEach { task ->
+                (task as? PatternFilterable)?.exclude(underProtocOutput)
+            }
+        }
     }
 }
 
diff --git a/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/ExcludeProtocOutputSpec.kt b/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/ExcludeProtocOutputSpec.kt
new file mode 100644
index 0000000000..52e77aff11
--- /dev/null
+++ b/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/ExcludeProtocOutputSpec.kt
@@ -0,0 +1,75 @@
+/*
+ * Copyright 2026, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package io.spine.tools.compiler.gradle.plugin
+
+import com.google.protobuf.gradle.ProtobufPlugin
+import io.kotest.matchers.shouldBe
+import java.io.File
+import org.gradle.api.internal.project.ProjectInternal
+import org.gradle.api.tasks.SourceSetContainer
+import org.gradle.api.tasks.compile.JavaCompile
+import org.gradle.kotlin.dsl.apply
+import org.gradle.testfixtures.ProjectBuilder
+import org.junit.jupiter.api.DisplayName
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+
+@DisplayName("The plugin should exclude the `protoc` output from compilation")
+internal class ExcludeProtocOutputSpec {
+
+    /**
+     * Reproduces the state in which the `protoc` output directory is among the
+     * source directories of the `main` source set, and verifies that the file it
+     * contains does not reach the `compileJava` task — see
+     * [issue #19](https://github.com/SpineEventEngine/compiler/issues/19).
+     */
+    @Test
+    fun `keeping it out of the Java compile task source`(@TempDir projectDir: File) {
+        val project = ProjectBuilder.builder().withProjectDir(projectDir).build()
+        project.group = "io.spine.stubs"
+        with(project) {
+            apply(plugin = "java")
+            apply<ProtobufPlugin>()
+            apply<Plugin>()
+            repositories.mavenLocal()
+        }
+
+        // A file under the default `protoc` output directory, added to the source set
+        // as if the source-set-level deduplication had not removed it.
+        val protocJavaDir = projectDir.resolve("build/generated/sources/proto/main/java")
+        protocJavaDir.mkdirs()
+        val leaked = protocJavaDir.resolve("Leaked.java")
+        leaked.writeText("class Leaked {}")
+        val sourceSets = project.extensions.getByType(SourceSetContainer::class.java)
+        sourceSets.getByName("main").java.srcDir(protocJavaDir)
+
+        (project as ProjectInternal).evaluate()
+
+        val compileJava = project.tasks.getByName("compileJava") as JavaCompile
+        compileJava.source.contains(leaked) shouldBe false
+    }
+}
diff --git a/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/PathsSpec.kt b/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/PathsSpec.kt
new file mode 100644
index 0000000000..4dd113b7ed
--- /dev/null
+++ b/gradle-plugin/src/test/kotlin/io/spine/tools/compiler/gradle/plugin/PathsSpec.kt
@@ -0,0 +1,68 @@
+/*
+ * Copyright 2026, TeamDev. All rights reserved.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * https://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Redistribution and use in source and/or binary forms, with or without
+ * modification, must retain the above copyright notice and the following
+ * disclaimer.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+ * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+ * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+ * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+ * OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+ * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+ * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+ * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+ * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+ * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ */
+
+package io.spine.tools.compiler.gradle.plugin
+
+import io.kotest.matchers.shouldBe
+import java.io.File
+import org.junit.jupiter.api.DisplayName
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.io.TempDir
+
+@DisplayName("`File.residesIn` should")
+internal class PathsSpec {
+
+    @Test
+    fun `treat a nested file as residing in the directory`(@TempDir dir: File) {
+        val root = dir.resolve("test").apply { mkdirs() }
+        val nested = root.resolve("java/Stub.java")
+
+        nested.residesIn(root) shouldBe true
+    }
+
+    @Test
+    fun `treat the directory itself as residing in it`(@TempDir dir: File) {
+        val root = dir.resolve("test").apply { mkdirs() }
+
+        root.residesIn(root) shouldBe true
+    }
+
+    @Test
+    fun `not treat a sibling directory as residing in it`(@TempDir dir: File) {
+        val test = dir.resolve("test").apply { mkdirs() }
+        val sibling = dir.resolve("test2").apply { mkdirs() }
+
+        sibling.residesIn(test) shouldBe false
+    }
+
+    @Test
+    fun `accept a directory that is already canonical`(@TempDir dir: File) {
+        val root = dir.resolve("test").apply { mkdirs() }
+        val nested = root.resolve("Stub.java")
+
+        nested.residesIn(root.canonicalFile.toPath()) shouldBe true
+    }
+}
diff --git a/version.gradle.kts b/version.gradle.kts
index 7d7b1687d5..a31766223d 100644
--- a/version.gradle.kts
+++ b/version.gradle.kts
@@ -30,10 +30,11 @@
  * This version is also used by integration test projects.
  * E.g. see `tests/consumer/build.gradle.kts`.
  */
-val compilerVersion: String by extra("2.0.0-SNAPSHOT.058")
+private val compilerVersion = "2.0.0-SNAPSHOT.059"
+extra.set("compilerVersion", compilerVersion)
 
 /**
  * The version, same as [compilerVersion], which is used for publishing
  * the Compiler Maven artifacts.
  */
-val versionToPublish by extra(compilerVersion)
+extra.set("versionToPublish", compilerVersion)