Checksum files within macOS app bundle dirs

We need to include these dirs so that the Updater can manage macOS apps
shipped as *part of* Fiji, rather than the toplevel Fiji dir itself
being a macOS app. These days, Apple's code-signing requirement makes it
nigh-impossible to have a self-modifying app bundle (which Fiji has been
until now). Simpler to ship a slim immutable signed Fiji.app that looks
for resources on the outside (i.e. `Fiji.app/..`).

Author: ctrueden

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

@@ -500,6 +500,17 @@ protected void initializeQueue() {
 		for (final String launcher : files.util.launchers)
 			queueIfExists(launcher);
 
+		// Queue any macOS .app folders.
+		File appDir = files.getAppRoot();
+		if (appDir != null) {
+			Set<String> allExtensions = Collections.singleton("");
+			for (File file : appDir.listFiles()) {
+				if (file.isDirectory() && file.getName().endsWith(".app")) {
+					queueDir(file.getName(), allExtensions);
+				}
+			}
+		}
+
 		for (int i = 0; i < directories.length; i += 2)
 			queueDir(directories[i], directories[i + 1]);
 

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

@@ -125,6 +125,10 @@ public FilesCollection(final LogService log, final File imagejRoot) {
 		updateSite.setOfficial(true);
 	}
 
+	public File getAppRoot() {
+		return imagejRoot;
+	}
+
 	public UpdateSite addUpdateSite(final String name, final String url,
 		final String sshHost, final String uploadDirectory, final long timestamp)
 	{