fix: restore executable permissions for filelist entries and formatting

Author: ih0r-d

org.graalvm.python.embedding/src/main/java/org/graalvm/python/embedding/VirtualFileSystemImpl.java

@@ -231,7 +231,11 @@ static FilelistEntry parse(String line) {
 
 			// v1 format: only absolute path
 			if (line.startsWith("/")) {
-				return new FilelistEntry(EntryType.FILE, line, DEFAULT_FILE_PERMISSIONS);
+				Set<PosixFilePermission> permissions = isExecutable(line)
+						? DEFAULT_DIR_PERMISSIONS // 0755
+						: DEFAULT_FILE_PERMISSIONS; // 0644
+
+				return new FilelistEntry(EntryType.FILE, line, permissions);
 			}
 
 			// v2 format: <type> <mode> <path>
@@ -275,6 +279,10 @@ private static String octalToSymbolic(String octal) {
 		}
 	}
 
+	private static boolean isExecutable(String resourcePath) {
+		return resourcePath.endsWith(".so") || resourcePath.endsWith(".sh") || resourcePath.contains("/bin/");
+	}
+
 	private final class FileEntry extends BaseEntry {
 		private byte[] data;
 		private List<FileEntry> toExtract;
@@ -538,7 +546,6 @@ private void initEntries() {
 		List<URL> filelistUrls = getFilelistURLs(filelistPath);
 		boolean hasNativeFiles = false;
 
-
 		fine("VFS fileslistPath = %s", filelistPath);
 		for (URL url : filelistUrls) {
 			try (InputStream stream = url.openStream()) {
@@ -593,7 +600,10 @@ private void initEntries() {
 
 						assert parent != null;
 						if (!platformPath.endsWith(PLATFORM_SEPARATOR)) {
-							FileEntry fileEntry = new FileEntry(platformPath, meta.permissions());
+							Set<PosixFilePermission> permissions = isExecutable(platformPath)
+									? DEFAULT_DIR_PERMISSIONS // 0755
+									: meta.permissions();
+							FileEntry fileEntry = new FileEntry(platformPath, permissions);
 							if (extractFilter != null && extractFilter.test(Paths.get(platformPath))) {
 								fileEntry.toExtract = List.of(fileEntry);
 							}