fix: improve fatjar export (jbangdev#2228)

Author: quintesse

src/main/java/dev/jbang/cli/Export.java

@@ -372,6 +372,17 @@ int apply(BuildContext ctx) throws IOException {
 					Util.verboseMsg("Unpacking artifact: " + dep);
 					UnpackUtil.unzip(dep.getFile(), tmpDir, false, null, ExportFatjar::handleExistingFile);
 				}
+				// Remove all signature files
+				Path metaInf = tmpDir.resolve("META-INF");
+				if (Files.exists(metaInf) && Files.isDirectory(metaInf)) {
+					try (DirectoryStream<Path> stream = Files.newDirectoryStream(metaInf, "*.{SF,DSA,RSA}")) {
+						for (Path entry : stream) {
+							Util.verboseMsg("Removing signature file: " + entry);
+							Files.delete(entry);
+						}
+					}
+				}
+				Util.verboseMsg("Creating jar: " + outputPath);
 				JarUtil.createJar(outputPath, tmpDir, null, prj.getMainClass(),
 						exportMixin.buildMixin.getProjectJdk(prj));
 			} finally {
@@ -389,6 +400,10 @@ int apply(BuildContext ctx) throws IOException {
 	}
 
 	public static void handleExistingFile(ZipFile zipFile, ZipArchiveEntry zipEntry, Path outFile) throws IOException {
+		if (Files.isDirectory(outFile) != zipEntry.isDirectory()) {
+			Util.warnMsg("Skipping conflicting duplicate file vs directory: " + zipEntry.getName());
+			return;
+		}
 		if (zipEntry.getName().startsWith("META-INF/services/")) {
 			Util.verboseMsg("Merging service files: " + zipEntry.getName());
 			try (ReadableByteChannel readableByteChannel = Channels.newChannel(zipFile.getInputStream(zipEntry));

src/main/java/dev/jbang/util/UnpackUtil.java

@@ -3,6 +3,7 @@
 import java.io.FileInputStream;
 import java.io.IOException;
 import java.io.InputStream;
+import java.nio.file.FileAlreadyExistsException;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -86,26 +87,40 @@ public static void unzip(Path zip, Path outputDir, boolean stripRootFolder, Path
 				if (!entry.startsWith(outputDir)) {
 					throw new IOException("Entry is outside of the target dir: " + zipEntry.getName());
 				}
-				if (zipEntry.isDirectory()) {
-					Files.createDirectories(entry);
-				} else if (zipEntry.isUnixSymlink()) {
-					Scanner s = new Scanner(zipFile.getInputStream(zipEntry)).useDelimiter("\\A");
-					String result = s.hasNext() ? s.next() : "";
-					Files.createSymbolicLink(entry, Paths.get(result));
-				} else {
-					if (!Files.isDirectory(entry.getParent())) {
-						Files.createDirectories(entry.getParent());
-					}
-					if (Files.isRegularFile(entry)) {
-						onExisting.handle(zipFile, zipEntry, entry);
+				try {
+					if (zipEntry.isDirectory() && checkValidParent(entry)) {
+						Files.createDirectories(entry);
+					} else if (zipEntry.isUnixSymlink()) {
+						Scanner s = new Scanner(zipFile.getInputStream(zipEntry)).useDelimiter("\\A");
+						String result = s.hasNext() ? s.next() : "";
+						Files.createSymbolicLink(entry, Paths.get(result));
 					} else {
-						defaultZipEntryCopy(zipFile, zipEntry, entry);
+						if (checkValidParent(entry.getParent())) {
+							Files.createDirectories(entry.getParent());
+						}
+						if (Files.exists(entry)) {
+							onExisting.handle(zipFile, zipEntry, entry);
+						} else {
+							defaultZipEntryCopy(zipFile, zipEntry, entry);
+						}
 					}
+				} catch (FileAlreadyExistsException e) {
+					onExisting.handle(zipFile, zipEntry, entry);
 				}
 			}
 		}
 	}
 
+	private static boolean checkValidParent(Path path) throws FileAlreadyExistsException {
+		while (path != null && !Files.exists(path)) {
+			path = path.getParent();
+		}
+		if (path != null && !Files.isDirectory(path)) {
+			throw new FileAlreadyExistsException("Parent path is not a directory: " + path);
+		}
+		return true;
+	}
+
 	public interface ExistingZipFileHandler {
 		void handle(ZipFile zipFile, ZipArchiveEntry zipEntry, Path outFile) throws IOException;
 	}