Set executable bit in a less fragile way

On my Ubuntu 24.04 system, I was seeing:

[ERROR] java.io.IOException: Cannot run program "chmod": error=13, Permission denied
	at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1170)
	at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1089)
	at java.base/java.lang.Runtime.exec(Runtime.java:681)
	at java.base/java.lang.Runtime.exec(Runtime.java:530)
	at net.imagej.updater.Installer.verify(Installer.java:389)
	at net.imagej.updater.Installer$VerifyFiles.itemDone(Installer.java:333)
	at net.imagej.updater.util.AbstractProgressable.itemDone(AbstractProgressable.java:87)
	at net.imagej.updater.util.Downloader.download(Downloader.java:130)
	at net.imagej.updater.util.Downloader.start(Downloader.java:90)
	at net.imagej.updater.Installer.start(Installer.java:217)
	at net.imagej.ui.swing.updater.UpdaterFrame.install(UpdaterFrame.java:596)
	at net.imagej.ui.swing.updater.UpdaterFrame$5.run(UpdaterFrame.java:534)
Caused by: java.io.IOException: error=13, Permission denied
	at java.base/java.lang.ProcessImpl.forkAndExec(Native Method)
	at java.base/java.lang.ProcessImpl.<init>(ProcessImpl.java:295)
	at java.base/java.lang.ProcessImpl.start(ProcessImpl.java:225)
	at java.base/java.lang.ProcessBuilder.start(ProcessBuilder.java:1126)
	... 11 more

Why? I have no idea. But using the setExecutable method instead works.

Author: ctrueden

src/main/java/net/imagej/updater/CommandLine.java

@@ -489,9 +489,8 @@ public void download(final FileObject file) {
 			new Downloader(progress).start(new OneFile(file));
 			if (file.executable && !Platforms.isWindows(files.platform())) {
 				try {
-					Runtime.getRuntime().exec(
-							new String[] { "chmod", "0755",
-									files.prefix(file.filename).getPath() });
+					// Use Java's native file permissions API instead of spawning chmod process
+					files.prefix(file.filename).setExecutable(true, false);
 				} catch (final Exception e) {
 					e.printStackTrace();
 					throw die("Could not mark " + file.filename

src/main/java/net/imagej/updater/Installer.java

@@ -385,10 +385,8 @@ public void verify(final Download download) {
 		file.setStatus(FileObject.Status.INSTALLED);
 
 		if (file.executable && !Platforms.isWindows(files.platform())) try {
-			Runtime.getRuntime()
-				.exec(
-					new String[] { "chmod", "0755",
-						download.destination.getAbsolutePath() });
+			// Use Java's native file permissions API instead of spawning chmod process
+			download.destination.setExecutable(true, false);
 		}
 		catch (final Exception e) {
 			files.log.error(e);