Add command to extract application in an optimized structure

This commit is a WIP that hacks the layertools jar to provide an
additional extract command that creates the following structure:

my-dir
├── application
│   └── my-app-1.0.0-SNAPSHOT.jar
├── dependencies
│   ├── ...
│   ├── spring-context-6.1.0-RC2.jar
│   ├── spring-context-support-6.1.0-RC2.jar
│   ├── ...
└── run-app.jar

With such a structure in place, the application can start with
`java -jar run-app.jar`.

Classes that were originally in `BOOT-INF/classes` are jared in the
`application` folder with the same name as the original repackaged jar.

Only dependencies that are listed in the `classpath.idx` file are
copied, and the `run-app.jar` contains a MANIFEST that list those libs
in the same order.

spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/ExtractJarCommand.java

@@ -0,0 +1,169 @@
+/*
+ * Copyright 2012-2023 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 org.springframework.boot.jarmode.layertools;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.attribute.BasicFileAttributeView;
+import java.nio.file.attribute.FileTime;
+import java.util.List;
+import java.util.Map;
+import java.util.jar.Attributes.Name;
+import java.util.jar.JarEntry;
+import java.util.jar.JarOutputStream;
+import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.springframework.boot.jarmode.layertools.JarStructure.Entry;
+import org.springframework.util.Assert;
+import org.springframework.util.StreamUtils;
+
+/**
+ * Hacking.
+ *
+ * @author Stephane Nicoll
+ */
+class ExtractJarCommand extends Command {
+
+	static final Option DESTINATION_OPTION = Option.of("destination", "string", "The destination to extract files to");
+
+	private final Context context;
+
+	private final JarStructure jarStructure;
+
+	ExtractJarCommand(Context context) {
+		this(context, IndexedJarStructure.get(context));
+	}
+
+	ExtractJarCommand(Context context, JarStructure jarStructure) {
+		super("extract2", "Extracts the application in optimized structure", Options.of(DESTINATION_OPTION),
+				Parameters.none());
+		this.context = context;
+		this.jarStructure = jarStructure;
+	}
+
+	@Override
+	protected void run(Map<Option, String> options, List<String> parameters) {
+		try {
+			Path destination = options.containsKey(DESTINATION_OPTION) ? Paths.get(options.get(DESTINATION_OPTION))
+					: this.context.getWorkingDir().toPath();
+			Path application = destination.resolve("application");
+			mkDirs(application);
+			Path applicationJarFile = application.resolve(this.context.getArchiveFile().getName());
+
+			Path dependencies = destination.resolve("dependencies");
+			mkDirs(dependencies);
+
+			try (JarOutputStream output = new JarOutputStream(Files.newOutputStream(applicationJarFile),
+					this.jarStructure.createApplicationJarManifest())) {
+				try (ZipInputStream zip = new ZipInputStream(new FileInputStream(this.context.getArchiveFile()))) {
+					ZipEntry zipEntry = zip.getNextEntry();
+					Assert.state(zipEntry != null, "File '" + this.context.getArchiveFile().toString()
+							+ "' is not compatible with layertools; ensure jar file is valid and launch script is not enabled");
+					while (zipEntry != null) {
+						Entry resolvedEntry = this.jarStructure.resolve(zipEntry);
+						if (resolvedEntry != null) {
+							if (resolvedEntry.library()) {
+								String location = "dependencies/" + resolvedEntry.location();
+								write(zip, zipEntry, destination, location);
+							}
+							else {
+								JarEntry jarEntry = createJarEntry(resolvedEntry, zipEntry);
+								output.putNextEntry(jarEntry);
+								StreamUtils.copy(zip, output);
+								output.closeEntry();
+							}
+						}
+						zipEntry = zip.getNextEntry();
+					}
+				}
+			}
+
+			// create the run-app.jar
+			createRunAppJar(destination, applicationJarFile);
+
+		}
+		catch (IOException ex) {
+			throw new IllegalStateException(ex);
+		}
+
+	}
+
+	private void createRunAppJar(Path destination, Path applicationJarFile) throws IOException {
+		Manifest manifest = this.jarStructure.createRunJarManifest((dependency) -> "dependencies/" + dependency);
+		String libs = manifest.getMainAttributes().getValue(Name.CLASS_PATH);
+		String applicationJar = destination.relativize(applicationJarFile).toString();
+		manifest.getMainAttributes().put(Name.CLASS_PATH, String.join(" ", applicationJar, libs));
+		Path runJar = destination.resolve("run-app.jar");
+		try (JarOutputStream output = new JarOutputStream(Files.newOutputStream(runJar), manifest)) {
+			// EMPTY
+		}
+	}
+
+	private void write(ZipInputStream zip, ZipEntry entry, Path destination, String name) throws IOException {
+		String canonicalOutputPath = destination.toFile().getCanonicalPath() + File.separator;
+		Path file = destination.resolve(name);
+		String canonicalEntryPath = file.toFile().getCanonicalPath();
+		Assert.state(canonicalEntryPath.startsWith(canonicalOutputPath),
+				() -> "Entry '" + entry.getName() + "' would be written to '" + canonicalEntryPath
+						+ "'. This is outside the output location of '" + canonicalOutputPath
+						+ "'. Verify the contents of your archive.");
+		mkParentDirs(file);
+		try (OutputStream out = Files.newOutputStream(file)) {
+			StreamUtils.copy(zip, out);
+		}
+		try {
+			Files.getFileAttributeView(file, BasicFileAttributeView.class)
+				.setTimes(entry.getLastModifiedTime(), entry.getLastAccessTime(), entry.getCreationTime());
+		}
+		catch (IOException ex) {
+			// File system does not support setting time attributes. Continue.
+		}
+	}
+
+	private static JarEntry createJarEntry(Entry resolvedEntry, ZipEntry originalEntry) {
+		JarEntry jarEntry = new JarEntry(resolvedEntry.location());
+		FileTime lastModifiedTime = originalEntry.getLastModifiedTime();
+		if (lastModifiedTime != null) {
+			jarEntry.setLastModifiedTime(lastModifiedTime);
+		}
+		FileTime lastAccessTime = originalEntry.getLastAccessTime();
+		if (lastAccessTime != null) {
+			jarEntry.setLastAccessTime(lastAccessTime);
+		}
+		FileTime creationTime = originalEntry.getCreationTime();
+		if (creationTime != null) {
+			jarEntry.setCreationTime(creationTime);
+		}
+		return jarEntry;
+	}
+
+	private static void mkParentDirs(Path file) throws IOException {
+		mkDirs(file.getParent());
+	}
+
+	private static void mkDirs(Path file) throws IOException {
+		Files.createDirectories(file);
+	}
+
+}

spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/IndexedJarStructure.java

@@ -0,0 +1,166 @@
+/*
+ * Copyright 2012-2023 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 org.springframework.boot.jarmode.layertools;
+
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.NoSuchFileException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.function.UnaryOperator;
+import java.util.jar.Attributes;
+import java.util.jar.Attributes.Name;
+import java.util.jar.JarFile;
+import java.util.jar.Manifest;
+import java.util.stream.Collectors;
+import java.util.zip.ZipEntry;
+
+import org.springframework.util.Assert;
+import org.springframework.util.StreamUtils;
+import org.springframework.util.StringUtils;
+
+/**
+ * {@link JarStructure} implementation backed by a {@code classpath.idx} file.
+ *
+ * @author Stephane Nicoll
+ */
+class IndexedJarStructure implements JarStructure {
+
+	private final Manifest originalManifest;
+
+	private final String libLocation;
+
+	private final String classesLocation;
+
+	private final List<String> classpathEntries;
+
+	IndexedJarStructure(Manifest originalManifest, String indexFile) {
+		this.originalManifest = originalManifest;
+		this.libLocation = getLocation(originalManifest, "Spring-Boot-Lib");
+		this.classesLocation = getLocation(originalManifest, "Spring-Boot-Classes");
+		this.classpathEntries = readIndexFile(indexFile);
+	}
+
+	private static String getLocation(Manifest manifest, String attribute) {
+		String location = getMandatoryAttribute(manifest, attribute);
+		if (!location.endsWith("/")) {
+			location = location + "/";
+		}
+		return location;
+	}
+
+	private static List<String> readIndexFile(String indexFile) {
+		String[] lines = Arrays.stream(indexFile.split("\n"))
+			.map((line) -> line.replace("\r", ""))
+			.filter(StringUtils::hasText)
+			.toArray(String[]::new);
+		List<String> classpathEntries = new ArrayList<>();
+		for (String line : lines) {
+			if (line.startsWith("- ")) {
+				classpathEntries.add(line.substring(3, line.length() - 1));
+			}
+			else {
+				throw new IllegalStateException("Classpath index file is malformed");
+			}
+		}
+		Assert.state(!classpathEntries.isEmpty(), "Empty classpath index file loaded");
+		return classpathEntries;
+	}
+
+	@Override
+	public Entry resolve(ZipEntry entry) {
+		if (entry.isDirectory()) {
+			return null;
+		}
+		String name = entry.getName();
+		if (this.classpathEntries.contains(name)) {
+			return new Entry(name, toStructureDependency(name), true);
+		}
+		else if (name.startsWith(this.classesLocation)) {
+			return new Entry(name, name.substring(this.classesLocation.length()), false);
+		}
+		return null;
+	}
+
+	@Override
+	public Manifest createRunJarManifest(UnaryOperator<String> libEntry) {
+		Manifest manifest = new Manifest();
+		Attributes attributes = manifest.getMainAttributes();
+		attributes.put(Name.MANIFEST_VERSION, "1.0");
+		attributes.put(Name.MAIN_CLASS, getMandatoryAttribute(this.originalManifest, "Start-Class"));
+		attributes.put(Name.CLASS_PATH,
+				this.classpathEntries.stream()
+					.map(this::toStructureDependency)
+					.map(libEntry)
+					.collect(Collectors.joining(" ")));
+		return manifest;
+	}
+
+	@Override
+	public Manifest createApplicationJarManifest() {
+		Manifest manifest = new Manifest();
+		Attributes attributes = manifest.getMainAttributes();
+		attributes.put(Name.MANIFEST_VERSION, "1.0");
+		copy(this.originalManifest, manifest, "Implementation-Title");
+		copy(this.originalManifest, manifest, "Implementation-Version");
+		return manifest;
+	}
+
+	private static void copy(Manifest left, Manifest right, String attribute) {
+		String value = left.getMainAttributes().getValue(attribute);
+		if (value != null) {
+			right.getMainAttributes().putValue(attribute, value);
+		}
+	}
+
+	private String toStructureDependency(String libEntryName) {
+		Assert.state(libEntryName.startsWith(this.libLocation), "Invalid library location " + libEntryName);
+		return libEntryName.substring(this.libLocation.length());
+	}
+
+	private static String getMandatoryAttribute(Manifest manifest, String attribute) {
+		String value = manifest.getMainAttributes().getValue(attribute);
+		if (value == null) {
+			throw new IllegalStateException("Manifest attribute '" + attribute + "' is mandatory");
+		}
+		return value;
+	}
+
+	static IndexedJarStructure get(Context context) {
+		try {
+			try (JarFile jarFile = new JarFile(context.getArchiveFile())) {
+				Manifest manifest = jarFile.getManifest();
+				String location = getMandatoryAttribute(manifest, "Spring-Boot-Classpath-Index");
+				ZipEntry entry = jarFile.getEntry(location);
+				if (entry != null) {
+					String indexFile = StreamUtils.copyToString(jarFile.getInputStream(entry), StandardCharsets.UTF_8);
+					return new IndexedJarStructure(manifest, indexFile);
+				}
+			}
+			return null;
+		}
+		catch (FileNotFoundException | NoSuchFileException ex) {
+			return null;
+		}
+		catch (IOException ex) {
+			throw new IllegalStateException(ex);
+		}
+	}
+
+}

spring-boot-project/spring-boot-tools/spring-boot-jarmode-layertools/src/main/java/org/springframework/boot/jarmode/layertools/JarStructure.java

@@ -0,0 +1,62 @@
+/*
+ * Copyright 2012-2023 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 org.springframework.boot.jarmode.layertools;
+
+import java.util.function.UnaryOperator;
+import java.util.jar.Manifest;
+import java.util.zip.ZipEntry;
+
+/**
+ * Provide information about a fat jar structure that is meant to be extracted.
+ *
+ * @author Stephane Nicoll
+ */
+interface JarStructure {
+
+	/**
+	 * Resolve the specified {@link ZipEntry}, return {@code null} if the entry should not
+	 * be handled.
+	 * @param entry the entry to handle
+	 * @return the resolved {@link Entry}
+	 */
+	Entry resolve(ZipEntry entry);
+
+	/**
+	 * Create the {@link Manifest} for the {@code run-jar} jar, applying the specified
+	 * operator on each classpath entry.
+	 * @param libEntry the operator to apply on each classpath entry
+	 * @return the manifest to use for the {@code run-jar} jar
+	 */
+	Manifest createRunJarManifest(UnaryOperator<String> libEntry);
+
+	/**
+	 * Create the {@link Manifest} for the jar that is created with classes and resources.
+	 * @return the manifest to use for the {@code application} jar
+	 */
+	Manifest createApplicationJarManifest();
+
+	/**
+	 * An entry to handle in the exploded structure.
+	 *
+	 * @param originalLocation the original location
+	 * @param location the relative location
+	 * @param library whether the entry refers to a library or a classpath resource
+	 */
+	record Entry(String originalLocation, String location, boolean library) {
+	}
+
+}