Rework entry ordering of repackaged archives

Previously, the Repackager would write entries in the following
order:

- Libraries that require unpacking
- Existing entries
    - Application classes
    - WEB-INF/lib jars in a war
- Libraries that do not require unpacking
- Loader classes

Libraries that require unpacking were written before existing entries
so that, when repackaging a war, an entry in WEB-INF/lib would not
get in first and prevent a library with same location from being
unpacked. However, this had the unwanted side-effect of changing
the classpath order when an entry requires unpacking.

This commit reworks the handling of existing entries and libraries
that require unpacking so that existing entries can be written first
while also marking any that match a library that requires unpacking
as requiring unpacking.

Additionally, loader classes are now written first. They are the
first classes in the jar that will be used so it seems to make sense
for them to appear first. This aligns Maven-based repackaging
with the Gradle plugin's behaviour and with the structure documented
in the reference documentation's "The Executable Jar Format" appendix.

The net result of the changes described above is that entries are
now written in the following order:

- Loader classes
- Existing entries
    - Application classes
    - WEB-INF/lib jars in a war marked for unpacking if needed
- Libraries

Closes gh-11695
Closes gh-11696

spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/test/java/org/springframework/boot/loader/tools/RepackagerTests.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2012-2017 the original author or authors.
+ * 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.
@@ -21,8 +21,10 @@ import java.io.File;
 import java.io.IOException;
 import java.nio.file.Files;
 import java.nio.file.attribute.PosixFilePermission;
+import java.util.ArrayList;
 import java.util.Calendar;
 import java.util.Enumeration;
+import java.util.List;
 import java.util.jar.Attributes;
 import java.util.jar.JarEntry;
 import java.util.jar.JarFile;
@@ -575,6 +577,58 @@ public class RepackagerTests {
 		}
 	}
 
+	@Test
+	public void loaderIsWrittenFirstThenApplicationClassesThenLibraries()
+			throws IOException {
+		this.testJarFile.addClass("com/example/Application.class",
+				ClassWithMainMethod.class);
+		File source = this.testJarFile.getFile();
+		File dest = this.temporaryFolder.newFile("dest.jar");
+		File libraryOne = createLibrary();
+		File libraryTwo = createLibrary();
+		File libraryThree = createLibrary();
+		Repackager repackager = new Repackager(source);
+		repackager.repackage(dest, (callback) -> {
+			callback.library(new Library(libraryOne, LibraryScope.COMPILE, false));
+			callback.library(new Library(libraryTwo, LibraryScope.COMPILE, true));
+			callback.library(new Library(libraryThree, LibraryScope.COMPILE, false));
+		});
+		assertThat(getEntryNames(dest)).containsSubsequence(
+				"org/springframework/boot/loader/",
+				"BOOT-INF/classes/com/example/Application.class",
+				"BOOT-INF/lib/" + libraryOne.getName(),
+				"BOOT-INF/lib/" + libraryTwo.getName(),
+				"BOOT-INF/lib/" + libraryThree.getName());
+	}
+
+	@Test
+	public void existingEntryThatMatchesUnpackLibraryIsMarkedForUnpack()
+			throws IOException {
+		File library = createLibrary();
+		this.testJarFile.addClass("WEB-INF/classes/com/example/Application.class",
+				ClassWithMainMethod.class);
+		this.testJarFile.addFile("WEB-INF/lib/" + library.getName(), library);
+		File source = this.testJarFile.getFile("war");
+		File dest = this.temporaryFolder.newFile("dest.war");
+		Repackager repackager = new Repackager(source);
+		repackager.setLayout(new Layouts.War());
+		repackager.repackage(dest, (callback) -> callback
+				.library(new Library(library, LibraryScope.COMPILE, true)));
+		assertThat(getEntryNames(dest)).containsSubsequence(
+				"org/springframework/boot/loader/",
+				"WEB-INF/classes/com/example/Application.class",
+				"WEB-INF/lib/" + library.getName());
+		JarEntry unpackLibrary = getEntry(dest, "WEB-INF/lib/" + library.getName());
+		assertThat(unpackLibrary.getComment()).startsWith("UNPACK:");
+	}
+
+	private File createLibrary() throws IOException {
+		TestJarFile library = new TestJarFile(this.temporaryFolder);
+		library.addClass("com/example/library/Library.class",
+				ClassWithoutMainMethod.class);
+		return library.getFile();
+	}
+
 	private boolean hasLauncherClasses(File file) throws IOException {
 		return hasEntry(file, "org/springframework/boot/")
 				&& hasEntry(file, "org/springframework/boot/loader/JarLauncher.class");
@@ -596,6 +650,17 @@ public class RepackagerTests {
 		}
 	}
 
+	private List<String> getEntryNames(File file) throws IOException {
+		List<String> entryNames = new ArrayList<>();
+		try (JarFile jarFile = new JarFile(file)) {
+			Enumeration<JarEntry> entries = jarFile.entries();
+			while (entries.hasMoreElements()) {
+				entryNames.add(entries.nextElement().getName());
+			}
+		}
+		return entryNames;
+	}
+
 	private static class MockLauncherScript implements LaunchScript {
 
 		private final byte[] bytes;