Ensure META-INF/MANIFEST.MF remains as first entry

Update Gradle archive tasks to ensure that `META-INF/` and
`META-INF/MANIFEST.MF` remain as the first entries of the archive.

Prior to this commit, rewritten archives would violate the implicit
specification of `JarInputStream` that these entries should be first.

Fixes gh-16698

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/main/java/org/springframework/boot/gradle/tasks/bundling/LoaderZipEntries.java

+/*
+ * Copyright 2012-2018 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.gradle.tasks.bundling;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.OutputStream;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
+
+import org.apache.commons.compress.archivers.zip.UnixStat;
+import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
+import org.apache.commons.compress.archivers.zip.ZipArchiveOutputStream;
+import org.gradle.api.file.FileTreeElement;
+import org.gradle.api.specs.Spec;
+
+/**
+ * Internal utility used to copy entries from the {@code spring-boot-loader.jar}.
+ *
+ * @author Andy Wilkinson
+ * @author Phillip Webb
+ */
+class LoaderZipEntries {
+
+	private Long entryTime;
+
+	LoaderZipEntries(Long entryTime) {
+		this.entryTime = entryTime;
+	}
+
+	public Spec<FileTreeElement> writeTo(ZipArchiveOutputStream zipOutputStream) throws IOException {
+		WrittenDirectoriesSpec writtenDirectoriesSpec = new WrittenDirectoriesSpec();
+		try (ZipInputStream loaderJar = new ZipInputStream(
+				getClass().getResourceAsStream("/META-INF/loader/spring-boot-loader.jar"))) {
+			java.util.zip.ZipEntry entry = loaderJar.getNextEntry();
+			while (entry != null) {
+				if (entry.isDirectory() && !entry.getName().equals("META-INF/")) {
+					writeDirectory(new ZipArchiveEntry(entry), zipOutputStream);
+					writtenDirectoriesSpec.add(entry);
+				}
+				else if (entry.getName().endsWith(".class")) {
+					writeClass(new ZipArchiveEntry(entry), loaderJar, zipOutputStream);
+				}
+				entry = loaderJar.getNextEntry();
+			}
+		}
+		return writtenDirectoriesSpec;
+	}
+
+	private void writeDirectory(ZipArchiveEntry entry, ZipArchiveOutputStream out) throws IOException {
+		prepareEntry(entry, UnixStat.DIR_FLAG | UnixStat.DEFAULT_DIR_PERM);
+		out.putArchiveEntry(entry);
+		out.closeArchiveEntry();
+	}
+
+	private void writeClass(ZipArchiveEntry entry, ZipInputStream in, ZipArchiveOutputStream out) throws IOException {
+		prepareEntry(entry, UnixStat.FILE_FLAG | UnixStat.DEFAULT_FILE_PERM);
+		out.putArchiveEntry(entry);
+		copy(in, out);
+		out.closeArchiveEntry();
+	}
+
+	private void prepareEntry(ZipArchiveEntry entry, int unixMode) {
+		if (this.entryTime != null) {
+			entry.setTime(this.entryTime);
+		}
+		entry.setUnixMode(unixMode);
+	}
+
+	private void copy(InputStream in, OutputStream out) throws IOException {
+		byte[] buffer = new byte[4096];
+		int bytesRead = -1;
+		while ((bytesRead = in.read(buffer)) != -1) {
+			out.write(buffer, 0, bytesRead);
+		}
+	}
+
+	/**
+	 * Spec to track directories that have been written.
+	 */
+	private static class WrittenDirectoriesSpec implements Spec<FileTreeElement> {
+
+		private final Set<String> entries = new HashSet<>();
+
+		@Override
+		public boolean isSatisfiedBy(FileTreeElement element) {
+			String path = element.getRelativePath().getPathString();
+			if (element.isDirectory() && !path.endsWith(("/"))) {
+				path += "/";
+			}
+			return this.entries.contains(path);
+		}
+
+		public void add(ZipEntry entry) {
+			this.entries.add(entry.getName());
+		}
+
+	}
+
+}

spring-boot-project/spring-boot-tools/spring-boot-gradle-plugin/src/test/java/org/springframework/boot/gradle/tasks/bundling/AbstractBootArchiveTests.java

@@ -17,6 +17,7 @@
 package org.springframework.boot.gradle.tasks.bundling;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
 import java.nio.file.Files;
@@ -34,6 +35,7 @@ import java.util.jar.JarFile;
 import java.util.jar.JarOutputStream;
 import java.util.jar.Manifest;
 import java.util.zip.ZipEntry;
+import java.util.zip.ZipInputStream;
 
 import org.apache.commons.compress.archivers.zip.ZipArchiveEntry;
 import org.apache.commons.compress.archivers.zip.ZipFile;
@@ -187,13 +189,18 @@ public abstract class AbstractBootArchiveTests<T extends Jar & BootArchive> {
 	}
 
 	@Test
-	public void loaderIsWrittenToTheRootOfTheJar() throws IOException {
+	public void loaderIsWrittenToTheRootOfTheJarAfterManifest() throws IOException {
 		this.task.setMainClassName("com.example.Main");
 		this.task.execute();
 		try (JarFile jarFile = new JarFile(this.task.getArchivePath())) {
 			assertThat(jarFile.getEntry("org/springframework/boot/loader/LaunchedURLClassLoader.class")).isNotNull();
 			assertThat(jarFile.getEntry("org/springframework/boot/loader/")).isNotNull();
 		}
+		// gh-16698
+		try (ZipInputStream zipInputStream = new ZipInputStream(new FileInputStream(this.task.getArchivePath()))) {
+			assertThat(zipInputStream.getNextEntry().getName()).isEqualTo("META-INF/");
+			assertThat(zipInputStream.getNextEntry().getName()).isEqualTo("META-INF/MANIFEST.MF");
+		}
 	}
 
 	@Test