Add apply command

Introduces the apply subcommand which formats Java source files in
place. FormattingService wraps the FileFormatter and takes a pre-scanned
file list so the directory scan is not repeated. Includes integration
tests covering default formatting, encoding, includes/excludes
filtering, and springjavaformatconfig discovery.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Author: timothysparg

spring-javaformat-cli/src/main/java/io/spring/javaformat/cli/SpringJavaFormatCommand.java

@@ -21,13 +21,16 @@
 import picocli.CommandLine.Model.CommandSpec;
 import picocli.CommandLine.Spec;
 
+import io.spring.javaformat.cli.format.ApplyCommand;
+
 /**
  * Root picocli command.
  *
  * @author Tim Sparg
  */
 @Component
 @Command(name = "spring-javaformat", mixinStandardHelpOptions = true, versionProvider = CliVersionProvider.class,
+		subcommands = { ApplyCommand.class },
 		description = "Formats and checks Java source files")
 @PicocliManaged
 class SpringJavaFormatCommand implements Runnable {

spring-javaformat-cli/src/main/java/io/spring/javaformat/cli/format/ApplyCommand.java

@@ -0,0 +1,99 @@
+/*
+ * Copyright 2017-present the original author or authors.
+ *
+ * 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
+ *
+ * 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 io.spring.javaformat.cli.format;
+
+import java.io.File;
+import java.io.PrintWriter;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.concurrent.Callable;
+
+import org.springframework.stereotype.Component;
+import picocli.CommandLine.Command;
+import picocli.CommandLine.Help.Ansi;
+import picocli.CommandLine.Mixin;
+import picocli.CommandLine.Model.CommandSpec;
+import picocli.CommandLine.Spec;
+
+import io.spring.javaformat.cli.InputOptions;
+import io.spring.javaformat.formatter.FileEdit;
+import io.spring.javaformat.formatter.FileFormatterException;
+
+/**
+ * Apply formatting command.
+ *
+ * @author Tim Sparg
+ */
+@Component
+@Command(name = "apply", mixinStandardHelpOptions = true, description = "Apply formatting to the codebase")
+public class ApplyCommand implements Callable<Integer> {
+
+	private static final Path CWD = Paths.get("").toAbsolutePath();
+
+	@Spec
+	private CommandSpec spec;
+
+	@Mixin
+	private InputOptions options;
+
+	private final FormattingService formattingService;
+
+	@SuppressWarnings("NullAway.Init")
+	ApplyCommand(FormattingService formattingService) {
+		this.formattingService = formattingService;
+	}
+
+	@Override
+	public Integer call() {
+		try {
+			this.formattingService.format(this.options).filter(FileEdit::hasEdits).forEach(this::save);
+			return 0;
+		}
+		catch (FileFormatterException ex) {
+			err().println(ansi(
+					"@|bold,red error:|@ unable to format file " + relativize(ex.getFile()) + ": " + ex.getMessage()));
+			return 1;
+		}
+	}
+
+	private PrintWriter err() {
+		return this.spec.commandLine().getErr();
+	}
+
+	private PrintWriter out() {
+		return this.spec.commandLine().getOut();
+	}
+
+	private void save(FileEdit edit) {
+		out().println(ansi("@|bold,green formatted|@  " + relativize(edit.getFile())));
+		edit.save();
+	}
+
+	private String ansi(String markup) {
+		return Ansi.AUTO.string(markup);
+	}
+
+	private static String relativize(File file) {
+		try {
+			return CWD.relativize(file.toPath().toAbsolutePath()).toString();
+		}
+		catch (IllegalArgumentException ex) {
+			return file.getAbsolutePath();
+		}
+	}
+
+}

spring-javaformat-cli/src/main/java/io/spring/javaformat/cli/format/FormattingService.java

@@ -0,0 +1,58 @@
+/*
+ * Copyright 2017-present the original author or authors.
+ *
+ * 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
+ *
+ * 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 io.spring.javaformat.cli.format;
+
+import java.io.File;
+import java.util.List;
+import java.util.stream.Stream;
+
+import org.springframework.stereotype.Component;
+
+import io.spring.javaformat.cli.InputOptions;
+import io.spring.javaformat.cli.scan.FileFormatterFactory;
+import io.spring.javaformat.cli.scan.FileScanner;
+import io.spring.javaformat.formatter.FileEdit;
+import io.spring.javaformat.formatter.FileFormatter;
+import io.spring.javaformat.formatter.FileFormatterException;
+
+/**
+ * Applies formatting to scanned files.
+ *
+ * @author Tim Sparg
+ */
+@Component
+public class FormattingService {
+
+	private final FileFormatterFactory fileFormatterFactory;
+
+	private final FileScanner fileScanner;
+
+	FormattingService(FileFormatterFactory fileFormatterFactory, FileScanner fileScanner) {
+		this.fileFormatterFactory = fileFormatterFactory;
+		this.fileScanner = fileScanner;
+	}
+
+	public Stream<FileEdit> format(InputOptions options) throws FileFormatterException {
+		return format(this.fileScanner.scan(options), options);
+	}
+
+	public Stream<FileEdit> format(List<File> files, InputOptions options) throws FileFormatterException {
+		FileFormatter formatter = this.fileFormatterFactory.create(options.path);
+		return formatter.formatFiles(files, options.encoding, options.resolveLineSeparator());
+	}
+
+}

spring-javaformat-cli/src/main/java/io/spring/javaformat/cli/format/package-info.java

@@ -0,0 +1,25 @@
+/*
+ * Copyright 2017-present the original author or authors.
+ *
+ * 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
+ *
+ * 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.
+ */
+
+/**
+ * Apply formatting command.
+ *
+ * @author Tim Sparg
+ */
+@NullMarked
+package io.spring.javaformat.cli.format;
+
+import org.jspecify.annotations.NullMarked;

spring-javaformat-cli/src/test/java/io/spring/javaformat/cli/AbstractCommandIntegrationTests.java

@@ -0,0 +1,69 @@
+/*
+ * Copyright 2017-present the original author or authors.
+ *
+ * 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
+ *
+ * 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 io.spring.javaformat.cli;
+
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.io.StringWriter;
+import java.io.UncheckedIOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.util.concurrent.Callable;
+import java.util.stream.Stream;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.boot.test.context.SpringBootTest;
+import org.springframework.boot.test.context.SpringBootTest.WebEnvironment;
+import picocli.CommandLine;
+import picocli.CommandLine.IFactory;
+
+/**
+ * Base class for command integration tests.
+ *
+ * @author Tim Sparg
+ */
+@SpringBootTest(webEnvironment = WebEnvironment.NONE)
+abstract class AbstractCommandIntegrationTests {
+
+	@Autowired
+	IFactory factory;
+
+	abstract Callable<Integer> command();
+
+	int execute(StringWriter out, StringWriter err, String... args) {
+		return new CommandLine(command(), this.factory).setOut(new PrintWriter(out))
+			.setErr(new PrintWriter(err))
+			.execute(args);
+	}
+
+	void copyFixture(Path fixturesDir, String name, Path target) throws IOException {
+		Path fixtureDir = fixturesDir.resolve(name);
+		try (Stream<Path> files = Files.walk(fixtureDir)) {
+			files.filter(Files::isRegularFile).forEach((source) -> {
+				try {
+					Path dest = target.resolve(fixtureDir.relativize(source));
+					Files.createDirectories(dest.getParent());
+					Files.copy(source, dest);
+				}
+				catch (IOException ex) {
+					throw new UncheckedIOException(ex);
+				}
+			});
+		}
+	}
+
+}

spring-javaformat-cli/src/test/java/io/spring/javaformat/cli/ApplyCommandIntegrationTests.java

@@ -0,0 +1,113 @@
+/*
+ * Copyright 2017-present the original author or authors.
+ *
+ * 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
+ *
+ * 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 io.spring.javaformat.cli;
+
+import java.io.StringWriter;
+import java.nio.charset.Charset;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+import org.junit.jupiter.api.Test;
+import org.junit.jupiter.api.io.TempDir;
+import org.springframework.beans.factory.annotation.Autowired;
+
+import io.spring.javaformat.cli.format.ApplyCommand;
+
+import static org.assertj.core.api.Assertions.assertThat;
+
+/**
+ * Integration tests for {@link ApplyCommand}.
+ *
+ * @author Tim Sparg
+ */
+class ApplyCommandIntegrationTests extends AbstractCommandIntegrationTests {
+
+	private static final Path FIXTURES_DIR = Path.of("src/test/resources/fixtures/format");
+
+	@Autowired
+	ApplyCommand applyCommand;
+
+	@Override
+	ApplyCommand command() {
+		return this.applyCommand;
+	}
+
+	@Test
+	void defaultEncodingFormatsFile(@TempDir Path tempDir) throws Exception {
+		copyFixture(FIXTURES_DIR, "default", tempDir);
+		String before = Files.readString(tempDir.resolve("Main.java"));
+
+		execute(new StringWriter(), new StringWriter(), tempDir.toString());
+
+		assertThat(Files.readString(tempDir.resolve("Main.java"))).isNotEqualTo(before);
+	}
+
+	@Test
+	void nonDefaultEncodingFormatsFile(@TempDir Path tempDir) throws Exception {
+		Charset latin1 = Charset.forName("ISO-8859-1");
+		copyFixture(FIXTURES_DIR, "latin1", tempDir);
+		String before = Files.readString(tempDir.resolve("Main.java"), latin1);
+
+		execute(new StringWriter(), new StringWriter(), "--encoding", "ISO-8859-1", tempDir.toString());
+
+		String after = Files.readString(tempDir.resolve("Main.java"), latin1);
+		assertThat(after).isNotEqualTo(before);
+		assertThat(after).contains("é");
+	}
+
+	@Test
+	void includesOnlyFormatsMatchingFiles(@TempDir Path tempDir) throws Exception {
+		copyFixture(FIXTURES_DIR, "default", tempDir);
+		String mainBefore = readFile(tempDir, "Main.java");
+		String noteBefore = Files.readString(tempDir.resolve("notes.txt"));
+		String excludedBefore = readFile(tempDir, "excluded/Excluded.java");
+
+		execute(new StringWriter(), new StringWriter(), "--includes", "**/Main.java", tempDir.toString());
+
+		assertThat(readFile(tempDir, "Main.java")).isNotEqualTo(mainBefore);
+		assertThat(Files.readString(tempDir.resolve("notes.txt"))).isEqualTo(noteBefore);
+		assertThat(readFile(tempDir, "excluded/Excluded.java")).isEqualTo(excludedBefore);
+	}
+
+	@Test
+	void excludesSkipsExcludedFiles(@TempDir Path tempDir) throws Exception {
+		copyFixture(FIXTURES_DIR, "default", tempDir);
+		String mainBefore = readFile(tempDir, "Main.java");
+		String excludedBefore = readFile(tempDir, "excluded/Excluded.java");
+
+		execute(new StringWriter(), new StringWriter(), "--excludes", "excluded/**", tempDir.toString());
+
+		assertThat(readFile(tempDir, "Main.java")).isNotEqualTo(mainBefore);
+		assertThat(readFile(tempDir, "excluded/Excluded.java")).isEqualTo(excludedBefore);
+	}
+
+	@Test
+	void springJavaFormatConfigChangesIndentationStyle(@TempDir Path tempDir) throws Exception {
+		copyFixture(FIXTURES_DIR, "spaces-config", tempDir);
+
+		execute(new StringWriter(), new StringWriter(), tempDir.toString());
+
+		String formatted = readFile(tempDir, "Main.java");
+		assertThat(formatted).contains("    void method() {");
+		assertThat(formatted).doesNotContain("\tvoid method() {");
+	}
+
+	private String readFile(Path dir, String path) throws Exception {
+		return Files.readString(dir.resolve(path));
+	}
+
+}

spring-javaformat-cli/src/test/resources/fixtures/format/default/Main.java

@@ -0,0 +1,4 @@
+class Unformatted {
+    void method() {
+    }
+}

spring-javaformat-cli/src/test/resources/fixtures/format/default/excluded/Excluded.java

@@ -0,0 +1,4 @@
+class Unformatted {
+    void method() {
+    }
+}

spring-javaformat-cli/src/test/resources/fixtures/format/default/notes.txt

@@ -0,0 +1 @@
+some notes