GH-719: Clear output directories when not using incremental compilation (#720)

When we are not performing incremental compilation, we should clear out
any output directories on each build before we process anything. This
prevents file removals between builds from producing invalid/unexpected
build results.

Fixes GH-719.

Author: ascopes

pom.xml

@@ -21,7 +21,7 @@
 
   <groupId>io.github.ascopes</groupId>
   <artifactId>protobuf-maven-plugin-parent</artifactId>
-  <version>3.5.1-SNAPSHOT</version>
+  <version>3.6.0-SNAPSHOT</version>
 
   <name>Protobuf Maven Plugin Parent</name>
   <description>Parent POM for the Protobuf Maven Plugin.</description>

protobuf-maven-plugin/pom.xml

@@ -22,7 +22,7 @@
   <parent>
     <groupId>io.github.ascopes</groupId>
     <artifactId>protobuf-maven-plugin-parent</artifactId>
-    <version>3.5.1-SNAPSHOT</version>
+    <version>3.6.0-SNAPSHOT</version>
   </parent>
 
   <artifactId>protobuf-maven-plugin</artifactId>

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/invoker.properties

@@ -0,0 +1,17 @@
+#
+# Copyright (C) 2023 - 2025, Ashley Scopes.
+#
+# 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
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+invoker.goals = clean package

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/pom.xml

@@ -0,0 +1,79 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!--
+
+    Copyright (C) 2023 - 2025, Ashley Scopes.
+
+    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
+
+    Unless required by applicable law or agreed to in writing, software
+    distributed under the License is distributed on an "AS IS" BASIS,
+    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+    See the License for the specific language governing permissions and
+    limitations under the License.
+
+-->
+<project xmlns="http://maven.apache.org/POM/4.0.0"
+  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+  xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+  <modelVersion>4.0.0</modelVersion>
+
+  <parent>
+    <groupId>@project.groupId@.it</groupId>
+    <artifactId>integration-test-parent</artifactId>
+    <version>@project.version@</version>
+    <relativePath>../setup/pom.xml</relativePath>
+  </parent>
+
+  <groupId>gh-719-clear-output-directories</groupId>
+  <artifactId>gh-719-clear-output-directories</artifactId>
+
+  <dependencies>
+    <dependency>
+      <groupId>com.google.protobuf</groupId>
+      <artifactId>protobuf-java</artifactId>
+      <scope>compile</scope>
+    </dependency>
+
+    <dependency>
+      <groupId>org.junit.jupiter</groupId>
+      <artifactId>junit-jupiter</artifactId>
+      <scope>test</scope>
+    </dependency>
+  </dependencies>
+
+  <build>
+    <plugins>
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-compiler-plugin</artifactId>
+      </plugin>
+
+      <plugin>
+        <groupId>org.apache.maven.plugins</groupId>
+        <artifactId>maven-surefire-plugin</artifactId>
+      </plugin>
+
+      <plugin>
+        <groupId>@project.groupId@</groupId>
+        <artifactId>@project.artifactId@</artifactId>
+
+        <configuration>
+          <cleanOutputDirectories>true</cleanOutputDirectories>
+          <incrementalCompilation>false</incrementalCompilation>
+        </configuration>
+
+        <executions>
+          <execution>
+            <goals>
+              <goal>generate</goal>
+            </goals>
+          </execution>
+        </executions>
+      </plugin>
+    </plugins>
+  </build>
+</project>

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/prebuild.groovy

@@ -0,0 +1,28 @@
+/*
+ * Copyright (C) 2023 - 2025, Ashley Scopes.
+ *
+ * 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
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+import java.nio.charset.StandardCharsets
+import java.nio.file.Files
+import java.nio.file.Path
+
+Path protobufDir = basedir.toPath()
+    .resolve("target")
+    .resolve("generated-sources")
+    .resolve("protobuf")
+Files.createDirectories(protobufDir)
+Files.writeString(protobufDir.resolve("Invalid.java"), "this will make compilation fail")
+
+return true

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/src/main/protobuf/helloworld.proto

@@ -0,0 +1,27 @@
+//
+// Copyright (C) 2023 - 2025, Ashley Scopes.
+//
+// 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
+//
+// Unless required by applicable law or agreed to in writing, software
+// distributed under the License is distributed on an "AS IS" BASIS,
+// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+// See the License for the specific language governing permissions and
+// limitations under the License.
+//
+
+syntax = "proto3";
+
+option java_multiple_files = true;
+option java_package = "org.example.helloworld";
+
+package org.example.helloworld;
+
+message GreetingRequest {
+  string name = 1;
+}
+

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/src/test/java/org/example/helloworld/ProtobufTest.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright (C) 2023 - 2025, Ashley Scopes.
+ *
+ * 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
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.example.helloworld;
+
+import static org.junit.jupiter.api.Assertions.assertEquals;
+import static org.junit.jupiter.api.Assertions.assertNotEquals;
+import static org.junit.jupiter.api.Assertions.assertTrue;
+
+import java.io.ByteArrayOutputStream;
+import java.util.ArrayList;
+import org.junit.jupiter.api.Test;
+
+class ProtobufTest {
+  @Test
+  void generatedProtobufSourcesAreFullMessages() throws Throwable {
+    // When
+    var superClasses = new ArrayList<String>();
+    Class<?> superClass = GreetingRequest.class;
+
+    do {
+      superClasses.add(superClass.getName());
+      superClass = superClass.getSuperclass();
+    } while (superClass != null);
+
+    // Then
+    // GeneratedMessageV3 for protobuf-java 3.25.3 and older.
+    // GeneratedMessage for protobuf-java 4.26.0 and newer.
+    assertTrue(superClasses.contains("com.google.protobuf.GeneratedMessage"));
+  }
+
+  @Test
+  void generatedProtobufSourcesAreValid() throws Throwable {
+    // Given
+    var expectedGreetingRequest = GreetingRequest
+        .newBuilder()
+        .setName("Ashley")
+        .build();
+
+    // When
+    var baos = new ByteArrayOutputStream();
+    expectedGreetingRequest.writeTo(baos);
+    var actualGreetingRequest = GreetingRequest.parseFrom(baos.toByteArray());
+
+    assertNotEquals(0, baos.toByteArray().length);
+
+    // Then
+    assertEquals(expectedGreetingRequest.getName(), actualGreetingRequest.getName());
+  }
+}

protobuf-maven-plugin/src/it/gh-719-clear-output-directories/test.groovy

@@ -0,0 +1,42 @@
+/*
+ * Copyright (C) 2023 - 2025, Ashley Scopes.
+ *
+ * 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
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+import java.nio.file.Path
+
+import static org.assertj.core.api.Assertions.assertThat
+
+Path baseDirectory = basedir.toPath().toAbsolutePath()
+Path generatedSourcesDir = baseDirectory.resolve("target/generated-sources/protobuf")
+Path classesDir = baseDirectory.resolve("target/classes")
+List<String> expectedGeneratedFiles = [
+    "org/example/helloworld/Helloworld",
+    "org/example/helloworld/GreetingRequest",
+    "org/example/helloworld/GreetingRequestOrBuilder",
+]
+
+assertThat(generatedSourcesDir).isDirectory()
+
+assertThat(classesDir).isDirectory()
+
+expectedGeneratedFiles.forEach {
+  assertThat(generatedSourcesDir.resolve("${it}.java"))
+      .exists()
+      .isNotEmptyFile()
+  assertThat(classesDir.resolve("${it}.class"))
+      .exists()
+      .isNotEmptyFile()
+}
+
+return true

protobuf-maven-plugin/src/main/java/io/github/ascopes/protobufmavenplugin/fs/FileUtils.java

@@ -22,10 +22,14 @@
 import java.io.OutputStream;
 import java.nio.file.FileSystem;
 import java.nio.file.FileSystemNotFoundException;
+import java.nio.file.FileVisitResult;
 import java.nio.file.Files;
+import java.nio.file.NoSuchFileException;
 import java.nio.file.OpenOption;
 import java.nio.file.Path;
+import java.nio.file.SimpleFileVisitor;
 import java.nio.file.StandardCopyOption;
+import java.nio.file.attribute.BasicFileAttributes;
 import java.nio.file.attribute.PosixFilePermission;
 import java.nio.file.spi.FileSystemProvider;
 import java.util.ArrayList;
@@ -35,6 +39,7 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.stream.Stream;
+import org.jspecify.annotations.Nullable;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -165,4 +170,32 @@ public static OutputStream newBufferedOutputStream(
   ) throws IOException {
     return new BufferedOutputStream(Files.newOutputStream(path, options));
   }
+
+  public static void deleteTree(Path path) throws IOException {
+    // Compared to checking if (!Files.exists(path)) first, this reduces the
+    // risk of other file-system based race conditions.
+    try {
+      Files.walkFileTree(path, new SimpleFileVisitor<Path>() {
+        @Override
+        public FileVisitResult visitFile(
+            Path file,
+            BasicFileAttributes attrs
+        ) throws IOException {
+          Files.deleteIfExists(file);
+          return FileVisitResult.CONTINUE;
+        }
+
+        @Override
+        public FileVisitResult postVisitDirectory(
+            Path directory,
+            @Nullable IOException ex
+        ) throws IOException {
+          Files.deleteIfExists(directory);
+          return FileVisitResult.CONTINUE;
+        }
+      });
+    } catch (NoSuchFileException ex) {
+      log.trace("Not deleting \"{}\", it does not exist", path, ex);
+    }
+  }
 }

protobuf-maven-plugin/src/main/java/io/github/ascopes/protobufmavenplugin/generation/GenerationRequest.java

@@ -232,6 +232,15 @@ public interface GenerationRequest {
    */
   OutputDescriptorAttachmentRegistrar getOutputDescriptorAttachmentRegistrar();
 
+  /**
+   * Whether to delete all output directories at the start of the build.
+   *
+   * <p>Ignored if using incremental compilation.
+   *
+   * @return the boolean preference.
+   */
+  boolean isCleanOutputDirectories();
+
   /**
    * Whether to include input {@code proto} sources in the output class
    * directory.