Allow prefixed bytes with fat JARs

Update `spring-boot-loader` ZIP processing code to support prefixed
bytes within the fat jar. This technique allows a bash script to be
embedded at the start of the JAR whilst still allowing `java -jar`
execution.

Fixes gh-1073

spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/CentralDirectoryEndRecord.java

@@ -87,6 +87,20 @@ class CentralDirectoryEndRecord {
 		return this.size == MINIMUM_SIZE + commentLength;
 	}
 
+	/**
+	 * Returns the location in the data that the archive actually starts. For most files
+	 * the archive data will start at 0, however, it is possible to have prefixed bytes
+	 * (often used for startup scripts) at the beginning of the data.
+	 * @param data the source data
+	 * @return the offset within the data where the archive begins
+	 */
+	public long getStartOfArchive(RandomAccessData data) {
+		long length = Bytes.littleEndianValue(this.block, this.offset + 12, 4);
+		long specifiedOffset = Bytes.littleEndianValue(this.block, this.offset + 16, 4);
+		long actualOffset = data.getSize() - this.size - length;
+		return actualOffset - specifiedOffset;
+	}
+
 	/**
 	 * Return the bytes of the "Central directory" based on the offset indicated in this
 	 * record.

spring-boot-tools/spring-boot-loader/src/main/java/org/springframework/boot/loader/jar/JarFile.java

@@ -119,15 +119,25 @@ public class JarFile extends java.util.jar.JarFile implements Iterable<JarEntryD
 	private JarFile(RandomAccessDataFile rootFile, String name, RandomAccessData data,
 			JarEntryFilter... filters) throws IOException {
 		super(rootFile.getFile());
+		CentralDirectoryEndRecord endRecord = new CentralDirectoryEndRecord(data);
+		this.data = getArchiveData(endRecord, data);
 		this.rootFile = rootFile;
 		this.name = name;
-		this.data = data;
 		this.size = data.getSize();
-		loadJarEntries(filters);
+		loadJarEntries(endRecord, filters);
 	}
 
-	private void loadJarEntries(JarEntryFilter[] filters) throws IOException {
+	private RandomAccessData getArchiveData(CentralDirectoryEndRecord endRecord,
-		CentralDirectoryEndRecord endRecord = new CentralDirectoryEndRecord(this.data);
+			RandomAccessData data) {
+		long offset = endRecord.getStartOfArchive(data);
+		if (offset == 0) {
+			return data;
+		}
+		return data.getSubsection(offset, data.getSize() - offset);
+	}
+
+	private void loadJarEntries(CentralDirectoryEndRecord endRecord,
+			JarEntryFilter[] filters) throws IOException {
 		RandomAccessData centralDirectory = endRecord.getCentralDirectory(this.data);
 		int numberOfRecords = endRecord.getNumberOfRecords();
 		this.entries = new ArrayList<JarEntryData>(numberOfRecords);

spring-boot-tools/spring-boot-loader/src/test/java/org/springframework/boot/loader/jar/JarFileTests.java

@@ -17,11 +17,14 @@
 package org.springframework.boot.loader.jar;
 
 import java.io.File;
+import java.io.FileInputStream;
 import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
 import java.io.IOException;
 import java.io.InputStream;
 import java.net.URL;
 import java.net.URLClassLoader;
+import java.nio.charset.Charset;
 import java.util.Enumeration;
 import java.util.jar.JarEntry;
 import java.util.jar.Manifest;
@@ -35,6 +38,8 @@ import org.junit.rules.TemporaryFolder;
 import org.springframework.boot.loader.TestJarCreator;
 import org.springframework.boot.loader.data.RandomAccessDataFile;
 import org.springframework.boot.loader.util.AsciiBytes;
+import org.springframework.util.FileCopyUtils;
+import org.springframework.util.StreamUtils;
 
 import static org.hamcrest.Matchers.equalTo;
 import static org.hamcrest.Matchers.greaterThan;
@@ -389,4 +394,18 @@ public class JarFileTests {
 		}
 		jarFile.close();
 	}
+
+	@Test
+	public void jarFileWithScriptAtTheStart() throws Exception {
+		File file = this.temporaryFolder.newFile();
+		InputStream sourceJarContent = new FileInputStream(this.rootJarFile);
+		FileOutputStream outputStream = new FileOutputStream(file);
+		StreamUtils.copy("#/bin/bash", Charset.defaultCharset(), outputStream);
+		FileCopyUtils.copy(sourceJarContent, outputStream);
+		this.rootJarFile = file;
+		this.jarFile = new JarFile(file);
+		// Call some other tests to verify
+		getEntries();
+		getNestedJarFile();
+	}
 }