Prevent duplicate jar entries from being written

Update the `AbstractJarWriter` so that it can directly build the layer
index as entries are written. Prior to this commit, a layer tracking
was handled by a decorator class which was broken because it didn't
override enough methods. Since `AbstractJarWriter` has quite a complex
API, it seems sensible to have it handle the layer index directly,
removing the need for a decorator entirely.

Fixes gh-23801

Author: philwebb

spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/AbstractJarWriter.java

@@ -60,6 +60,20 @@ public abstract class AbstractJarWriter implements LoaderClassesWriter {
 
 	private final Set<String> writtenEntries = new HashSet<>();
 
+	private Layers layers;
+
+	private LayersIndex layersIndex;
+
+	/**
+	 * Update this writer to use specific layers.
+	 * @param layers the layers to use
+	 * @param layersIndex the layers index to update
+	 */
+	void useLayers(Layers layers, LayersIndex layersIndex) {
+		this.layers = layers;
+		this.layersIndex = layersIndex;
+	}
+
 	/**
 	 * Write the specified manifest.
 	 * @param manifest the manifest to write
@@ -89,7 +103,7 @@ final void writeEntries(JarFile jarFile, EntryTransformer entryTransformer, Unpa
 				EntryWriter entryWriter = new InputStreamEntryWriter(inputStream);
 				JarArchiveEntry transformedEntry = entryTransformer.transform(entry);
 				if (transformedEntry != null) {
-					writeEntry(transformedEntry, entryWriter, unpackHandler);
+					writeEntry(transformedEntry, entryWriter, unpackHandler, true);
 				}
 			}
 		}
@@ -144,7 +158,15 @@ public void writeNestedLibrary(String location, Library library) throws IOExcept
 		entry.setTime(getNestedLibraryTime(library));
 		new CrcAndSize(library::openStream).setupStoredEntry(entry);
 		try (InputStream inputStream = library.openStream()) {
-			writeEntry(entry, new InputStreamEntryWriter(inputStream), new LibraryUnpackHandler(library));
+			writeEntry(entry, new InputStreamEntryWriter(inputStream), new LibraryUnpackHandler(library), false);
+			updateLayerIndex(entry.getName(), library);
+		}
+	}
+
+	private void updateLayerIndex(String name, Library library) {
+		if (this.layers != null) {
+			Layer layer = this.layers.getLayer(library);
+			this.layersIndex.add(layer, name);
 		}
 	}
 
@@ -225,7 +247,7 @@ private boolean isClassEntry(JarEntry entry) {
 	}
 
 	private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter) throws IOException {
-		writeEntry(entry, entryWriter, UnpackHandler.NEVER);
+		writeEntry(entry, entryWriter, UnpackHandler.NEVER, true);
 	}
 
 	/**
@@ -234,10 +256,11 @@ private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter) throws I
 	 * @param entry the entry to write
 	 * @param entryWriter the entry writer or {@code null} if there is no content
 	 * @param unpackHandler handles possible unpacking for the entry
+	 * @param updateLayerIndex if the layer index should be updated
 	 * @throws IOException in case of I/O errors
 	 */
-	private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter, UnpackHandler unpackHandler)
-			throws IOException {
+	private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter, UnpackHandler unpackHandler,
+			boolean updateLayerIndex) throws IOException {
 		String name = entry.getName();
 		writeParentDirectoryEntries(name);
 		if (this.writtenEntries.add(name)) {
@@ -248,18 +271,28 @@ private void writeEntry(JarArchiveEntry entry, EntryWriter entryWriter, UnpackHa
 				entry.setSize(entryWriter.size());
 			}
 			entryWriter = addUnpackCommentIfNecessary(entry, entryWriter, unpackHandler);
+			if (updateLayerIndex) {
+				updateLayerIndex(entry);
+			}
 			writeToArchive(entry, entryWriter);
 		}
 	}
 
+	private void updateLayerIndex(JarArchiveEntry entry) {
+		if (this.layers != null && !entry.getName().endsWith("/")) {
+			Layer layer = this.layers.getLayer(entry.getName());
+			this.layersIndex.add(layer, entry.getName());
+		}
+	}
+
 	protected abstract void writeToArchive(ZipEntry entry, EntryWriter entryWriter) throws IOException;
 
 	private void writeParentDirectoryEntries(String name) throws IOException {
 		String parent = name.endsWith("/") ? name.substring(0, name.length() - 1) : name;
 		while (parent.lastIndexOf('/') != -1) {
 			parent = parent.substring(0, parent.lastIndexOf('/'));
 			if (!parent.isEmpty()) {
-				writeEntry(new JarArchiveEntry(parent + "/"), null, UnpackHandler.NEVER);
+				writeEntry(new JarArchiveEntry(parent + "/"), null, UnpackHandler.NEVER, false);
 			}
 		}
 	}

spring-boot-project/spring-boot-tools/spring-boot-loader-tools/src/main/java/org/springframework/boot/loader/tools/Packager.java

@@ -29,7 +29,6 @@
 import java.util.jar.JarFile;
 import java.util.jar.Manifest;
 import java.util.stream.Collectors;
-import java.util.zip.ZipEntry;
 
 import org.apache.commons.compress.archivers.jar.JarArchiveEntry;
 
@@ -168,9 +167,7 @@ protected final boolean isAlreadyPackaged(File file) throws IOException {
 	protected final void write(JarFile sourceJar, Libraries libraries, AbstractJarWriter writer) throws IOException {
 		Assert.notNull(libraries, "Libraries must not be null");
 		WritableLibraries writeableLibraries = new WritableLibraries(libraries);
-		if (this.layers != null) {
-			writer = new LayerTrackingEntryWriter(writer);
-		}
+		writer.useLayers(this.layers, this.layersIndex);
 		writer.writeManifest(buildManifest(sourceJar));
 		writeLoaderClasses(writer);
 		writer.writeEntries(sourceJar, getEntityTransformer(), writeableLibraries);
@@ -422,35 +419,6 @@ private boolean isTransformable(JarArchiveEntry entry) {
 
 	}
 
-	/**
-	 * Decorator to track the layers as entries are written.
-	 */
-	private final class LayerTrackingEntryWriter extends AbstractJarWriter {
-
-		private final AbstractJarWriter writer;
-
-		private LayerTrackingEntryWriter(AbstractJarWriter writer) {
-			this.writer = writer;
-		}
-
-		@Override
-		public void writeNestedLibrary(String location, Library library) throws IOException {
-			this.writer.writeNestedLibrary(location, library);
-			Layer layer = Packager.this.layers.getLayer(library);
-			Packager.this.layersIndex.add(layer, location + library.getName());
-		}
-
-		@Override
-		protected void writeToArchive(ZipEntry entry, EntryWriter entryWriter) throws IOException {
-			this.writer.writeToArchive(entry, entryWriter);
-			if (!entry.getName().endsWith("/")) {
-				Layer layer = Packager.this.layers.getLayer(entry.getName());
-				Packager.this.layersIndex.add(layer, entry.getName());
-			}
-		}
-
-	}
-
 	/**
 	 * An {@link UnpackHandler} that determines that an entry needs to be unpacked if a
 	 * library that requires unpacking has a matching entry name.