MLE-21542 First batch of null checks

The one in AbstractCommand should knock out a lot of warnings.

Author: rjrudin

ml-app-deployer/src/main/java/com/marklogic/appdeployer/command/AbstractCommand.java

@@ -478,7 +478,8 @@ protected File[] listFilesInDirectory(File dir) {
 		if (files != null && files.length > 1) {
 			Arrays.sort(files);
 		}
-		return files;
+		// dir.listFiles is allowed to return null, so we do this so callers don't have to worry about null.
+		return files != null ? files : new File[0];
 	}
 
 	protected void logResourceDirectoryNotFound(File dir) {

ml-app-deployer/src/main/java/com/marklogic/appdeployer/command/AbstractResourceCommand.java

@@ -212,8 +212,11 @@ protected File[] listFilesInDirectory(File resourceDir, CommandContext context)
 	public void undo(CommandContext context) {
 		if (deleteResourcesOnUndo) {
 			setIncrementalMode(false);
-			for (File resourceDir : getResourceDirs(context)) {
-				processUndoOnResourceDir(context, resourceDir);
+			File[] dirs = getResourceDirs(context);
+			if (dirs != null) {
+				for (File resourceDir : dirs) {
+					processUndoOnResourceDir(context, resourceDir);
+				}
 			}
 		}
 	}

ml-app-deployer/src/main/java/com/marklogic/mgmt/selector/AbstractNameMatchingResourceSelector.java

@@ -74,7 +74,7 @@ protected void selectAmps(MapResourceSelection selection, ManageClient manageCli
 			Namespace ns = Namespace.getNamespace("http://marklogic.com/manage/security");
 			for (Element amp : amps.getListItems()) {
 				String nameref = amp.getChildText("nameref", ns);
-				if (nameMatches(nameref)) {
+				if (nameref != null && nameMatches(nameref)) {
 					String uriref = amp.getChildText("uriref", ns);
 					selection.select(MapResourceSelection.AMPS, uriref);
 				}