Support Jar file data prefixes when exporting

For cases like Jar2Exe

recaf-core/src/main/java/software/coley/recaf/info/properties/builtin/ZipPrefixDataProperty.java

@@ -0,0 +1,58 @@
+package software.coley.recaf.info.properties.builtin;
+
+import jakarta.annotation.Nonnull;
+import jakarta.annotation.Nullable;
+import software.coley.recaf.info.Info;
+import software.coley.recaf.info.properties.BasicProperty;
+import software.coley.recaf.info.properties.Property;
+
+/**
+ * Built in property to track data appearing before the ZIP header in an archive.
+ *
+ * @author Matt Coley
+ */
+public class ZipPrefixDataProperty extends BasicProperty<byte[]> {
+	public static final String KEY = "zip-prefix-data";
+
+	/**
+	 * @param data
+	 * 		Optional data.
+	 */
+	public ZipPrefixDataProperty(@Nullable byte[] data) {
+		super(KEY, data);
+	}
+
+	/**
+	 * @param info
+	 * 		Info instance.
+	 *
+	 * @return Optional data.
+	 * {@code null} when no property value is assigned.
+	 */
+	@Nullable
+	public static byte[] get(@Nonnull Info info) {
+		Property<byte[]> property = info.getProperty(KEY);
+		if (property != null) {
+			return property.value();
+		}
+		return null;
+	}
+
+	/**
+	 * @param info
+	 * 		Info instance.
+	 * @param value
+	 * 		Optional data.
+	 */
+	public static void set(@Nonnull Info info, @Nonnull byte[] value) {
+		info.setProperty(new ZipPrefixDataProperty(value));
+	}
+
+	/**
+	 * @param info
+	 * 		Info instance.
+	 */
+	public static void remove(@Nonnull Info info) {
+		info.removeProperty(KEY);
+	}
+}

recaf-core/src/main/java/software/coley/recaf/services/workspace/io/BasicResourceImporter.java

@@ -7,6 +7,7 @@
 import software.coley.lljzip.format.model.CentralDirectoryFileHeader;
 import software.coley.lljzip.format.model.ZipArchive;
 import software.coley.lljzip.util.ExtraFieldTime;
+import software.coley.lljzip.util.MemorySegmentUtil;
 import software.coley.recaf.analytics.logging.Logging;
 import software.coley.recaf.info.*;
 import software.coley.recaf.info.builder.FileInfoBuilder;
@@ -21,6 +22,7 @@
 
 import java.io.File;
 import java.io.IOException;
+import java.lang.foreign.MemorySegment;
 import java.net.URL;
 import java.nio.file.*;
 import java.nio.file.attribute.BasicFileAttributes;
@@ -130,11 +132,17 @@ private WorkspaceFileResource handleZip(WorkspaceFileResourceBuilder builder, Zi
 		ZipArchive archive = config.mapping().apply(source.readAll());
 
 		// Sanity check, if there's data at the head of the file AND its otherwise empty its probably junk.
-		if (archive.getPrefixData() != null && archive.getEnd() != null && archive.getParts().size() == 1) {
+		MemorySegment prefixData = archive.getPrefixData();
+		if (prefixData != null && archive.getEnd() != null && archive.getParts().size() == 1) {
 			// We'll throw as the caller should catch this case and handle it based on their needs.
 			throw new IOException("Content matched ZIP header but had no file entries");
 		}
 
+		// Record prefix data to attribute held by the zip file info.
+		if (prefixData != null) {
+			ZipPrefixDataProperty.set(zipInfo, MemorySegmentUtil.toByteArray(prefixData));
+		}
+
 		// Build model from the contained files in the ZIP
 		archive.getLocalFiles().forEach(header -> {
 			LocalFileHeaderSource headerSource = new LocalFileHeaderSource(header, isAndroid);

recaf-core/src/main/java/software/coley/recaf/services/workspace/io/WorkspaceExportOptions.java

@@ -3,9 +3,9 @@
 import jakarta.annotation.Nonnull;
 import software.coley.recaf.info.*;
 import software.coley.recaf.info.properties.builtin.*;
+import software.coley.recaf.services.workspace.WorkspaceManager;
 import software.coley.recaf.util.Unchecked;
 import software.coley.recaf.util.ZipCreationUtils;
-import software.coley.recaf.services.workspace.WorkspaceManager;
 import software.coley.recaf.workspace.model.Workspace;
 import software.coley.recaf.workspace.model.bundle.AndroidClassBundle;
 import software.coley.recaf.workspace.model.bundle.JvmClassBundle;
@@ -18,6 +18,7 @@
 import java.io.InputStream;
 import java.nio.file.Files;
 import java.nio.file.Path;
+import java.nio.file.StandardOpenOption;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.TreeMap;
@@ -136,6 +137,7 @@ private class WorkspaceExporterImpl implements WorkspaceExporter {
 		private final Map<String, Long> modifyTimes = new HashMap<>();
 		private final Map<String, Long> createTimes = new HashMap<>();
 		private final Map<String, Long> accessTimes = new HashMap<>();
+		private byte[] prefix;
 
 		@Override
 		public void export(@Nonnull Workspace workspace) throws IOException {
@@ -163,7 +165,12 @@ public void export(@Nonnull Workspace workspace) throws IOException {
 					});
 
 					// Write buffer to path
-					Files.write(path, zipBuilder.bytes());
+					if (prefix != null) {
+						Files.write(path, prefix);
+						Files.write(path, zipBuilder.bytes(), StandardOpenOption.APPEND);
+					} else {
+						Files.write(path, zipBuilder.bytes());
+					}
 					break;
 				case DIRECTORY:
 					for (Map.Entry<String, byte[]> entry : contents.entrySet()) {
@@ -186,12 +193,19 @@ public void export(@Nonnull Workspace workspace) throws IOException {
 		 * 		Workspace to pull data from.
 		 */
 		private void populate(@Nonnull Workspace workspace) {
+			// If shading libs, they go first so the primary content will be the authoritative copy for
+			// any duplicate paths held by both resources.
 			if (bundleSupporting) {
 				for (WorkspaceResource supportingResource : workspace.getSupportingResources()) {
 					mapInto(contents, supportingResource);
 				}
 			}
-			mapInto(contents, workspace.getPrimaryResource());
+			WorkspaceResource primary = workspace.getPrimaryResource();
+			mapInto(contents, primary);
+
+			// If the resource had prefix data, get it here so that we can write it back later.
+			if (primary instanceof WorkspaceFileResource resource)
+				prefix = ZipPrefixDataProperty.get(resource.getFileInfo());
 		}
 
 		/**