/* ###
 * IP: GHIDRA
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package ghidra.app.util.headless;

import java.io.*;
import java.net.*;
import java.util.*;
import java.util.regex.Pattern;

import org.apache.commons.io.FilenameUtils;

import generic.jar.ResourceFile;
import generic.stl.Pair;
import generic.util.Path;
import ghidra.GhidraApplicationLayout;
import ghidra.GhidraJarApplicationLayout;
import ghidra.app.plugin.core.analysis.AutoAnalysisManager;
import ghidra.app.plugin.core.osgi.BundleHost;
import ghidra.app.script.*;
import ghidra.app.script.JythonStubScriptProvider.JythonStubException;
import ghidra.app.util.headless.HeadlessScript.HeadlessContinuationOption;
import ghidra.app.util.importer.ProgramLoader;
import ghidra.app.util.opinion.*;
import ghidra.formats.gfilesystem.*;
import ghidra.framework.*;
import ghidra.framework.client.ClientUtil;
import ghidra.framework.client.RepositoryAdapter;
import ghidra.framework.data.*;
import ghidra.framework.main.AppInfo;
import ghidra.framework.model.*;
import ghidra.framework.project.DefaultProject;
import ghidra.framework.project.DefaultProjectManager;
import ghidra.framework.protocol.ghidra.*;
import ghidra.framework.protocol.ghidra.GhidraURLQuery.LinkFileControl;
import ghidra.framework.remote.User;
import ghidra.framework.store.LockException;
import ghidra.framework.store.local.LocalFileSystem;
import ghidra.program.database.ProgramContentHandler;
import ghidra.program.model.address.AddressSetView;
import ghidra.program.model.listing.Program;
import ghidra.program.util.GhidraProgramUtilities;
import ghidra.program.util.ProgramLocation;
import ghidra.util.*;
import ghidra.util.classfinder.ClassSearcher;
import ghidra.util.exception.*;
import ghidra.util.task.TaskMonitor;
import utilities.util.FileUtilities;

/**
 * The class used kick-off and interact with headless processing.  All headless options have been
 * broken out into their own class: {@link HeadlessOptions}.  This class is intended to be used
 * one of two ways:
 * <ul>
 *   <li>Used by {@link AnalyzeHeadless} to perform headless analysis based on arguments specified
 *   on the command line.</li>
 *   <li>Used by another tool as a library to perform headless analysis.</li>
 * </ul>
 * <p>
 * Note: This class is not thread safe.
 */
public class HeadlessAnalyzer {

	private static HeadlessAnalyzer instance;

	private HeadlessOptions options;
	private HeadlessGhidraProjectManager projectManager;
	private Project project;
	private boolean analysisTimedOut;
	private DomainFolder saveDomainFolder;
	private Map<String, Object> storage;
	private URLClassLoader classLoaderForDotClassScripts;
	private FileSystemService fsService;

	/**
	 * Gets a headless analyzer, initializing the application if necessary with the specified
	 * logging parameters.  An {@link IllegalStateException} will be thrown if the application has
	 * already been initialized or a headless analyzer has already been retrieved.  In these cases,
	 * the headless analyzer should be gotten with {@link HeadlessAnalyzer#getInstance()}.
	 * 
	 * @param logFile The desired application log file.  If null, the default application log file
	 *   will be used (see {@link Application#initializeLogging}).
	 * @param scriptLogFile The desired scripting log file.  If null, the default scripting log file
	 *   will be used (see {@link Application#initializeLogging}).
	 * @param useLog4j true if log4j is to be used; otherwise, false.  If this class is being used by
	 *     another tool as a library, using log4j might interfere with that tool.
	 * @return An instance of a new headless analyzer.
	 * @throws IllegalStateException if an application or headless analyzer instance has already been initialized.
	 * @throws IOException if there was a problem reading the application.properties file.
	 */
	public static HeadlessAnalyzer getLoggableInstance(File logFile, File scriptLogFile,
			boolean useLog4j) throws IllegalStateException, IOException {

		// Prevent more than one headless analyzer from being instantiated.  Too much about it
		// messes with global system settings, so under the current design of Ghidra, allowing
		// more than one to exist could result in unpredictable behavior.
		if (instance != null) {
			throw new IllegalStateException(
				"A headless analzyer instance has already been retrieved.  " +
					"Use HeadlessAnalyzer.getInstance() to get it.");
		}

		// Cannot set logging because application has already been initialized.
		if (Application.isInitialized()) {
			throw new IllegalStateException(
				"Logging cannot be set because the application has already been initialized.  " +
					"Use HeadlessAnalyzer.getInstance() to get the headless analyzer.");
		}

		// Initialize application with the provided logging parameters
		ApplicationConfiguration configuration = new HeadlessGhidraApplicationConfiguration();
		if (useLog4j) {
			if (logFile != null) {
				configuration.setApplicationLogFile(logFile);
			}
			if (scriptLogFile != null) {
				configuration.setScriptLogFile(scriptLogFile);
			}
		}
		else {
			configuration.setInitializeLogging(false);
			Msg.setErrorLogger(new HeadlessErrorLogger(logFile));
		}
		Application.initializeApplication(getApplicationLayout(), configuration);

		// Instantiate and return singleton headless analyzer
		instance = new HeadlessAnalyzer();
		return instance;
	}

	/**
	 * Gets a headless analyzer instance, with the assumption that the application has already been
	 * initialized.  If this is called before the application has been initialized, it will
	 * initialize the application with no logging.
	 * 
	 * @return An instance of a new headless analyzer.
	 * @throws IOException if there was a problem reading the application.properties file (only possible
	 *     if the application had not be initialized).
	 */
	public static HeadlessAnalyzer getInstance() throws IOException {

		// Prevent more than one headless analyzer from being instantiated.  Too much about it
		// messes with global system settings, so under the current design of Ghidra, allowing
		// more than one to exist could result in unpredictable behavior.
		if (instance != null) {
			return instance;
		}

		// Initialize application (if necessary)
		if (!Application.isInitialized()) {
			ApplicationConfiguration configuration = new HeadlessGhidraApplicationConfiguration();
			configuration.setInitializeLogging(false);
			Msg.setErrorLogger(new HeadlessErrorLogger(null));
			Application.initializeApplication(getApplicationLayout(), configuration);
		}

		// Instantiate and return singleton headless analyzer
		instance = new HeadlessAnalyzer();
		return instance;
	}

	/**
	 * Gets the appropriate Ghidra application layout for this headless analyzer.
	 * <p>
	 * The headless analyzer can be used in both "normal" mode and single jar mode, so
	 * we need to use the appropriate layout for either case.
	 * 
	 * @return The appropriate Ghidra application layout for this headless analyzer.
	 * @throws IOException if there was a problem getting an appropriate application layout.
	 */
	private static GhidraApplicationLayout getApplicationLayout() throws IOException {
		GhidraApplicationLayout layout;
		try {
			layout = new GhidraApplicationLayout();
		}
		catch (IOException e) {
			Msg.debug(HeadlessAnalyzer.class,
				"Unable to load the standard Ghidra application layout. " + e.getMessage() +
					".  Attempting to load the Ghidra Jar application layout.");
			layout = new GhidraJarApplicationLayout();
		}
		return layout;
	}

	/**
	 * Creates a new headless analyzer object with default settings.
	 */
	private HeadlessAnalyzer() {
		// Create default options which the caller can later set prior to processing.
		options = new HeadlessOptions();

		// Ghidra URL handler registration.  There's no harm in doing this more than once.
		Handler.registerHandler();

		// Ensure that we are running in "headless mode",  preventing Swing-based methods from
		// running (causing headless operation to lose focus).
		System.setProperty("java.awt.headless", "true");
		System.setProperty(SystemUtilities.HEADLESS_PROPERTY, Boolean.TRUE.toString());

		// Put analyzer in its default state
		reset();

		// Initialize FileSytemService
		fsService = FileSystemService.getInstance();
	}

	/**
	 * Resets the state of the headless analyzer to the default settings.
	 */
	public void reset() {
		options.reset();
		project = null;
		analysisTimedOut = false;
		saveDomainFolder = null;
		storage = new HashMap<>();
		classLoaderForDotClassScripts = null;
	}

	/**
	 * Gets the headless analyzer's options.
	 * 
	 * @return The headless analyer's options.
	 */
	public HeadlessOptions getOptions() {
		return options;
	}

	/**
	 * Process the optional import file/directory list and process each imported file:
	 * <ol>
	 * <li>execute ordered list of pre-scripts</li>
	 * <li>perform auto-analysis if not disabled</li>
	 * <li>execute ordered list of post-scripts</li>
	 * </ol>
	 * If no import files or directories have been specified the ordered list
	 * of pre/post scripts will be executed once.
	 * 
	 * @param ghidraURL ghidra URL for existing server repository and optional
	 *                  folder path
	 * @param filesToImport directories and files to be imported (null or empty
	 *                      is acceptable if we are in -process mode)
	 * @throws IOException if there was an IO-related problem
	 * @throws MalformedURLException specified URL is invalid
	 * @throws URISyntaxException specified URL is invalid
	 */
	public void processURL(URL ghidraURL, List<File> filesToImport)
			throws IOException, MalformedURLException, URISyntaxException {

		if (options.readOnly && options.commit) {
			Msg.error(this,
				"Abort due to Headless analyzer error: The requested readOnly option is in conflict " +
					"with the commit option");
			return;
		}

		if (!"ghidra".equals(ghidraURL.getProtocol())) {
			throw new MalformedURLException("Unsupported repository URL: " + ghidraURL);
		}

		if (GhidraURL.isLocalURL(ghidraURL)) {
			Msg.error(this,
				"Ghidra URL command form does not supported local project URLs (ghidra:/path...)");
			return;
		}

		String path = ghidraURL.getPath();
		if (path == null) {
			throw new MalformedURLException("Unsupported repository URL: " + ghidraURL);
		}

		path = path.trim();
		if (path.length() == 0) {
			throw new MalformedURLException("Unsupported repository URL: " + ghidraURL);
		}

		if (!options.runScriptsNoImport) { // Running in -import mode
			if ((filesToImport == null || filesToImport.size() == 0) &&
				options.preScripts.isEmpty() && options.postScripts.isEmpty()) {
				Msg.warn(this, "REPORT: Nothing to do ... must specify files for import.");
				return;
			}
		}

		BundleHost bundleHost = GhidraScriptUtil.acquireBundleHostReference();
		bundleHost.add(parseScriptPaths(options.scriptPaths), true, true);
		try {
			showConfiguredScriptPaths();
			compileScripts();

			Msg.info(HeadlessAnalyzer.class, "HEADLESS: execution starts");

			// force explicit folder access since file may have same name as folder
			ghidraURL = GhidraURL.getFolderURL(ghidraURL);

			Msg.info(this, "Opening ghidra repository folder: " + ghidraURL);

			GhidraURLQuery.queryRepositoryUrl(ghidraURL, options.readOnly,
				new GhidraURLResultHandlerAdapter() {

					@Override
					public void processResult(DomainFolder domainFolder, URL url,
							TaskMonitor monitor) throws IOException, CancelledException {
						try {
							project = new HeadlessProject(getProjectManager(),
								domainFolder.getProjectData());

							if (!checkUpdateOptions()) {
								return; // TODO: Should an exception be thrown?
							}

							if (options.runScriptsNoImport) {
								processNoImport(domainFolder.getPathname());
							}
							else {
								processWithImport(domainFolder.getPathname(), filesToImport);
							}
						}
						finally {
							if (project != null) {
								project.close();
							}
						}
					}

					@Override
					public void handleError(String title, String message, URL url,
							IOException cause) throws IOException {
						if (cause instanceof FileNotFoundException) {
							throw new IOException("Connect to repository folder failed");
						}
						if (cause != null) {
							throw cause;
						}
						throw new IOException(title + ": " + message);
					}

					// Link files are skipped to avoid duplicate processing
					// Processing should be done on actual folder - not a linked folder
				}, LinkFileControl.NO_FOLLOW, TaskMonitor.DUMMY);

		}
		catch (CancelledException e) {
			throw new IOException(e); // unexpected
		}
		finally {
			GhidraScriptUtil.releaseBundleHostReference();
		}
	}

	/**
	 * Process the optional import file/directory list and process each imported file:
	 * <ol>
	 * <li>execute ordered list of pre-scripts</li>
	 * <li>perform auto-analysis if not disabled</li>
	 * <li>execute ordered list of post-scripts</li>
	 * </ol>
	 * If no import files or directories have been specified the ordered list
	 * of pre/post scripts will be executed once.
	 * 
	 * @param projectLocation directory path of project
	 * 						  If project exists it will be opened, otherwise it will be created.
	 * @param projectName project name
	 * @param rootFolderPath root folder for imports
	 * @param filesToImport directories and files to be imported (null or empty is acceptable if
	 *        				we are in -process mode)
	 * @throws IOException if there was an IO-related problem.  If caused by a failure to obtain a
	 * write-lock on the project the exception cause will a {@code LockException}.
	 */
	public void processLocal(String projectLocation, String projectName, String rootFolderPath,
			List<File> filesToImport) throws IOException {

		if (options.readOnly && options.commit) {
			Msg.error(this,
				"Abort due to Headless analyzer error: The requested readOnly option is " +
					"in conflict with the commit option");
			return;
		}

		// If not importing, remove trailing slash so that non-existent folders aren't created
		if (options.runScriptsNoImport) {
			if ((rootFolderPath.endsWith("/")) && (rootFolderPath.length() > 1)) {
				rootFolderPath = rootFolderPath.substring(0, rootFolderPath.length() - 1);
			}
		}
		else {
			// If we are importing, need some files to import or at least a script to run!
			if ((filesToImport == null || filesToImport.size() == 0) &&
				options.preScripts.isEmpty() && options.postScripts.isEmpty()) {
				Msg.warn(this, "REPORT: Nothing to do ... must specify file(s) for import.");
				return;
			}

			// If importing, add trailing slash if it isn't there so that non-existent folders are created
			if (!rootFolderPath.endsWith("/")) {
				rootFolderPath += "/";
			}
		}

		BundleHost bundleHost = GhidraScriptUtil.acquireBundleHostReference();
		bundleHost.add(parseScriptPaths(options.scriptPaths), true, true);
		try {
			showConfiguredScriptPaths();
			compileScripts();

			Msg.info(HeadlessAnalyzer.class, "HEADLESS: execution starts");

			File dir = new File(projectLocation);
			ProjectLocator locator = new ProjectLocator(dir.getAbsolutePath(), projectName);

			if (locator.getProjectDir().exists()) {
				project = openProject(locator);
			}
			else {
				if (options.runScriptsNoImport) {
					Msg.error(this, "Could not find project: " + locator +
						" -- should already exist in -process mode.");
					throw new IOException("Could not find project: " + locator);
				}

				if (!options.runScriptsNoImport && options.readOnly) {
					// assume temporary when importing with readOnly option
					options.deleteProject = true;
				}

				Msg.info(this, "Creating " + (options.deleteProject ? "temporary " : "") +
					"project: " + locator);
				project = getProjectManager().createProject(locator, null, false);
			}

			try {

				if (!checkUpdateOptions()) {
					return; // TODO: Should an exception be thrown?
				}

				if (options.runScriptsNoImport) {
					processNoImport(rootFolderPath);
				}
				else {
					processWithImport(rootFolderPath, filesToImport);
				}
			}
			finally {
				project.close();
				if (!options.runScriptsNoImport && options.deleteProject) {
					FileUtilities.deleteDir(locator.getProjectDir());
					locator.getMarkerFile().delete();
				}
			}
		}
		finally {
			GhidraScriptUtil.releaseBundleHostReference();
		}
	}

	/**
	 * Checks to see if the most recent analysis timed out.
	 * 
	 * @return true if the most recent analysis timed out; otherwise, false.
	 */
	public boolean checkAnalysisTimedOut() {
		return analysisTimedOut;
	}

	void setSaveFolder(DomainFolder domFolder) {
		saveDomainFolder = domFolder;

		if (domFolder != null) {
			Msg.info(this, "Save location changed to: " + domFolder.getPathname());
		}
	}

	void addVariableToStorage(String nameOfVar, Object valOfVar) {
		if (storage.containsKey(nameOfVar)) {
			Msg.warn(this, "Overwriting existing storage variable: " + nameOfVar);
		}

		storage.put(nameOfVar, valOfVar);
	}

	Set<String> getStorageKeys() {
		return storage.keySet();
	}

	Object getVariableFromStorage(String nameOfVar) {
		if (!storage.containsKey(nameOfVar)) {
			Msg.warn(this, "The storage variable '" + nameOfVar +
				"' does not exist in HeadlessAnalyzer storage.");
			return null;
		}

		return storage.get(nameOfVar);
	}

	/**
	 * Get/Create specified folder path within project
	 * 
	 * @param folderPath the folder path within the project
	 * @param create if true, folder will be created if it does not exist
	 * @return DomainFolder for specified path
	 * @throws InvalidNameException if folder name is invalid
	 * @throws IOException if folder can not be created
	 */
	DomainFolder getDomainFolder(String folderPath, boolean create)
			throws IOException, InvalidNameException {

		DomainFolder domFolder = project.getProjectData().getFolder(folderPath);

		if (create && domFolder == null) {
			// Create any folder that doesn't exist
			String cleanPath = folderPath.replaceAll("^" + DomainFolder.SEPARATOR + "+", "");
			cleanPath = cleanPath.replaceAll(DomainFolder.SEPARATOR + "+$", "");

			String[] subfolders = cleanPath.split(DomainFolder.SEPARATOR + "+");

			int folderIndex = 0;
			String currPath = DomainFolder.SEPARATOR + subfolders[folderIndex];

			DomainFolder testFolder = project.getProjectData().getFolder(currPath);
			DomainFolder baseFolder = null;

			// Stay in loop while we see folders that exist
			while ((testFolder != null) && (folderIndex < (subfolders.length - 1))) {
				folderIndex++;
				baseFolder = testFolder;
				testFolder = baseFolder.getFolder(subfolders[folderIndex]);
			}

			// If none of the folders exist, create new files starting from the root
			if (folderIndex == 0) {
				baseFolder = project.getProjectData().getRootFolder();
			}

			// Since this method is only called by import, we create any folder that
			// does not exist.
			for (int i = folderIndex; i < subfolders.length; i++) {
				baseFolder = baseFolder.createFolder(subfolders[i]);
				Msg.info(this, "Created project folder: " + subfolders[i]);
			}

			domFolder = baseFolder;
		}

		return domFolder;
	}

	boolean storageContainsKey(String nameOfVar) {
		return storage.containsKey(nameOfVar);
	}

	/**
	 * Runs the specified script with the specified state.
	 * 
	 * @param scriptState State representing environment variables that the script is able
	 * 					  to access.
	 * @param script Script to be run.
	 * @return  whether the script successfully completed running
	 */
	private boolean runScript(GhidraState scriptState, GhidraScript script) {
		if (script instanceof HeadlessScript) {
			((HeadlessScript) script).setHeadlessInstance(this);
		}

		ResourceFile srcFile = script.getSourceFile();
		String scriptName =
			srcFile != null ? srcFile.getAbsolutePath() : (script.getClass().getName() + ".class");

		try {
			Msg.info(this, "SCRIPT: " + scriptName);

			// Execute the script, but don't directly write to stdout or stderr. The headless
			// analyzer only uses the logging mechanism to get output to the user.
			script.execute(scriptState, ScriptControls.NONE);
		}
		catch (Exception exc) {
			String logErrorMsg = "REPORT SCRIPT ERROR: ";
			Msg.error(this, logErrorMsg, exc);
			return false;
		}

		return true;
	}

	/**
	 * Check file update options (i.e., readOnly, commit) and change defaults if needed.
	 * @return true if OK to continue
	 */
	private boolean checkUpdateOptions() {

		if (options.readOnly) {
			String readOnlyError =
				"Abort due to Headless analyzer error: The requested -readOnly option " +
					"is in conflict with the ";

			if (options.commit) {
				Msg.error(this, readOnlyError + "-commit option.");
				return false;
			}

			if (options.okToDelete) {
				Msg.error(this, readOnlyError + "-okToDelete option.");
				return false;
			}
		}
		else if (!isInWritableProject()) {
			Msg.error(this, "Processing files within read-only project/repository " +
				"- the -readOnly option is required.");
			return false;
		}

		boolean commitAllowed = isCommitAllowed();
		if (options.commit && !commitAllowed) {
			Msg.error(this,
				"Commit to repository not possible (due to permission or connection issue)");
			return false;
		}

		if (project.getProjectLocator().isTransient()) {
			if (!options.commit) {
				if (commitAllowed && !options.readOnly) {
					Msg.info(this,
						"When processing a URL, -commit is automatically enabled unless -readOnly mode " +
							"is specified.  Enabling -commit and continuing.");
					options.commit = true;
				}
			}
		}

		if (options.overwrite) {
			boolean isImport = !options.runScriptsNoImport;
			if (!isImport) {
				Msg.info(this,
					"Ignoring -overwrite because it is not applicable to -process mode.");
			}
			else if (options.readOnly) {
				Msg.info(this,
					"Ignoring -overwrite because it is not applicable to -readOnly import mode.");
				options.overwrite = false;
			}
		}

		return true;
	}

	private boolean isInWritableProject() {
		return project.getProjectData().getRootFolder().isInWritableProject();
	}

	private boolean isCommitAllowed() {
		RepositoryAdapter repository = project.getRepository();
		if (repository == null) {
			return true;
		}
		try {
			repository.connect();
			if (!repository.isConnected()) {
				return false;
			}
			User user = repository.getUser();
			if (!user.hasWritePermission()) {
				Msg.error(this, "User '" + user.getName() +
					"' does not have write permission to repository - commit not allowed");
				return false;
			}
			return true;
		}
		catch (IOException e) {
			Msg.error(this, "Repository connection failed (" + repository.getServerInfo() +
				") - commit not allowed");
			return false;
		}
	}

	private List<ResourceFile> parseScriptPaths(List<String> scriptPaths) {
		if (scriptPaths == null) {
			return List.of();
		}
		List<ResourceFile> parsedScriptPaths = new ArrayList<>();
		for (String path : scriptPaths) {
			ResourceFile pathFile = Path.fromPathString(path);
			if (pathFile.exists()) {
				parsedScriptPaths.add(pathFile);
			}
			else {
				Msg.warn(this, "REPORT: Could not find -scriptPath entry, skipping: " + pathFile);
			}
		}
		return parsedScriptPaths;
	}

	private void showConfiguredScriptPaths() {
		StringBuffer buf = new StringBuffer("HEADLESS Script Paths:");
		for (ResourceFile dir : GhidraScriptUtil.getScriptSourceDirectories()) {
			buf.append("\n    ");
			buf.append(dir.getAbsolutePath());
		}
		Msg.info(HeadlessAnalyzer.class, buf.toString());
	}

	private ResourceFile findScript(String scriptName) {
		ResourceFile scriptSource = new ResourceFile(scriptName);
		scriptSource = scriptSource.getCanonicalFile();
		if (scriptSource.exists()) {
			return scriptSource;
		}
		scriptSource = GhidraScriptUtil.findScriptByName(scriptName);
		if (scriptSource != null) {
			return scriptSource;
		}
		throw new IllegalArgumentException("Script not found: " + scriptName);
	}

	/**
	 * Checks the script name to ensure it exists. If the script type has a GhidraScriptProvider
	 * (any type of script but .class), then return the ResourceFile that represents that script.
	 * 
	 * If the script is a class file, return null (one class loader is stored to allow the
	 * Headless Analyzer to find all the class files).
	 * 
	 * GhidraScript is not instantiated here, because it is important that each script be
	 * instantiated at the time it's used. If a GhidraScript object is re-used, this causes
	 * problems where GhidraScript variables aren't being re-initialized at each use of the script.
	 * 
	 * @param scriptName The name of the script to check
	 * @return ResourceFile representing the source file, or null (if script is a .class file)
	 */
	private ResourceFile checkScript(String scriptName) {

		// Check for pre-compiled GhidraScript (e.g., my.package.Impl.class)
		String classExtension = ".class";

		if (scriptName.endsWith(classExtension)) {
			String className =
				scriptName.substring(0, scriptName.length() - classExtension.length());
			try {

				// Create a classloader that contains all the ghidra_script paths (especially the one
				// specified in -scriptPath!)
				List<ResourceFile> dirs = GhidraScriptUtil.getScriptSourceDirectories();
				List<URL> urls = new ArrayList<>();

				for (ResourceFile dir : dirs) {
					try {
						urls.add(dir.toURL());
					}
					catch (MalformedURLException e) {
						// Do nothing. If can't make a URL out of the dir, don't add it.
					}
				}

				classLoaderForDotClassScripts =
					URLClassLoader.newInstance(urls.toArray(new URL[0]));

				ClassSearcher.forNameSafe(className, GhidraScript.class,
					classLoaderForDotClassScripts);

				// No issues, but return null, which signifies we don't actually have a
				// ResourceFile to associate with the script name
				return null;
			}
			catch (ClassNotFoundException e) {
				Msg.error(this,
					"REPORT SCRIPT ERROR: java class not found for '" + className + "'");
			}
			catch (ClassCastException e) {
				Msg.error(this,
					"REPORT SCRIPT ERROR: java class '" + className + "' is not a GhidraScript");
			}
			throw new IllegalArgumentException("Invalid script: " + scriptName);
		}

		try {
			ResourceFile scriptSource = findScript(scriptName);
			GhidraScriptProvider provider = GhidraScriptUtil.getProvider(scriptSource);

			if (provider == null) {
				throw new IOException("Missing plugin needed to run scripts of this type. Please " +
					"ensure you have installed the necessary plugin.");
			}

			return scriptSource;
		}
		catch (Exception | NoClassDefFoundError exc) {
			String logErrorMsg = "REPORT SCRIPT ERROR: " + scriptName + " : " + exc.getMessage();
			Msg.error(this, logErrorMsg);
		}
		throw new IllegalArgumentException("Invalid script: " + scriptName);
	}

	/**
	 * Creates mapping from script name to actual Script object
	 * 
	 * @param scriptsList  List of scripts
	 * @return  mapping of script name to its associated Script object
	 */
	private Map<String, ResourceFile> checkScriptsList(List<Pair<String, String[]>> scriptsList) {
		Map<String, ResourceFile> map = new HashMap<>();
		for (Pair<String, String[]> scriptPair : scriptsList) {
			String scriptName = scriptPair.first;
			ResourceFile scriptFile = checkScript(scriptName);
			map.put(scriptName, scriptFile);
		}
		return map;
	}

	private void compileScripts() throws IOException {

		// Check that given locations for .properties files are valid
		if (options.propertiesFileStrPaths.size() > 0) {

			options.propertiesFilePaths.clear();

			for (String path : options.propertiesFileStrPaths) {
				Path currPath = new Path(path, true, false, true);

				ResourceFile resource = currPath.getPath();

				if (!resource.isDirectory()) {
					throw new IOException("Properties file path: '" + path +
						"' either does not exist, " + "or is not a valid directory.");
				}

				if (currPath.isEnabled() && !options.propertiesFilePaths.contains(resource)) {
					options.propertiesFilePaths.add(resource);
				}
			}
		}

		if (options.preScriptFileMap == null) {
			options.preScriptFileMap = checkScriptsList(options.preScripts);
		}

		if (options.postScriptFileMap == null) {
			options.postScriptFileMap = checkScriptsList(options.postScripts);
		}
	}

	/**
	 * Run a list of scripts
	 * 
	 * @param scriptsList  list of script names to run
	 * @param scriptFileMap    mapping of script names to Script objects
	 * @param scriptState  the GhidraState to be passed into each script
	 * @param continueOption option that could have been set by script(s)
	 * @return option that could have been set by script(s)
	 */
	private HeadlessContinuationOption runScriptsList(List<Pair<String, String[]>> scriptsList,
			Map<String, ResourceFile> scriptFileMap, GhidraState scriptState,
			HeadlessContinuationOption continueOption) {

		ResourceFile currScriptFile;
		HeadlessContinuationOption retOption = continueOption;

		boolean scriptSuccess;
		boolean isHeadlessScript = false;
		String scriptName = "";
		GhidraScript currScript;

		try {
			for (Pair<String, String[]> scriptPair : scriptsList) {
				scriptName = scriptPair.first;
				String[] scriptArgs = scriptPair.second;

				StringBuilder buf = new StringBuilder();
				for (String arg : scriptArgs) {
					buf.append("'");
					buf.append(arg);
					buf.append("' ");
				}
				Msg.info(this, "REPORT: Execute script: " + scriptName + " " + buf.toString());

				// For .class files, there is no ResourceFile mapping. Need to load from the
				// stored 'classLoaderForDotClassScripts'
				if (scriptName.endsWith(".class")) {

					if (classLoaderForDotClassScripts == null) {
						throw new IllegalArgumentException("Invalid script: " + scriptName);
					}

					String className = scriptName.substring(0, scriptName.length() - 6);
					Class<? extends GhidraScript> c = ClassSearcher.forNameSafe(className,
						GhidraScript.class, classLoaderForDotClassScripts);

					// Get parent folder to pass to GhidraScript
					File parentFile = new File(c.getResource(c.getSimpleName() + ".class").toURI())
							.getParentFile();

					currScript = c.getConstructor().newInstance();
					currScript.setScriptArgs(scriptArgs);

					if (options.propertiesFilePaths.size() > 0) {
						currScript.setPotentialPropertiesFileLocations(options.propertiesFilePaths);
					}

					currScript.setPropertiesFileLocation(parentFile.getAbsolutePath(), className);
				}
				else {
					currScriptFile = scriptFileMap.get(scriptName);

					// GhidraScriptProvider case
					GhidraScriptProvider provider = GhidraScriptUtil.getProvider(currScriptFile);
					PrintWriter errWriter = new PrintWriter(System.err);
					currScript = provider.getScriptInstance(currScriptFile, errWriter);
					currScript.setScriptArgs(scriptArgs);

					if (options.propertiesFilePaths.size() > 0) {
						currScript.setPotentialPropertiesFileLocations(options.propertiesFilePaths);
					}
				}

				isHeadlessScript = currScript instanceof HeadlessScript ? true : false;

				if (isHeadlessScript) {
					((HeadlessScript) currScript).setInitialContinuationOption(retOption);
				}

				scriptSuccess = runScript(scriptState, currScript);

				if (isHeadlessScript) {
					if (scriptSuccess) {
						retOption = ((HeadlessScript) currScript).getContinuationOption();

						// If script wants to abort, return without running any scripts that follow
						if ((retOption == HeadlessContinuationOption.ABORT) ||
							(retOption == HeadlessContinuationOption.ABORT_AND_DELETE)) {
							return retOption;
						}

					}
					else {
						// If script did not run successfully, abort further processing automatically
						Msg.warn(this,
							"Script does not exist or encountered problems; further processing is aborted.");

						return HeadlessContinuationOption.ABORT;
					}
				}
			}
		}
		catch (JythonStubException e) {
			// We want to effectively exit with an error code, but this class may be used as a 
			// Ghidra library method in some scenarios, so System.exit(1) is too aggressive.
			// Throwing an Error allows Ghidra to exit with an uncaught exception when run from
			// the command line, but allows for the possibility of a library client to handle
			// the problem in a way that better suits their application.
			throw new Error(e);
		}
		catch (Exception exc) {
			String logErrorMsg = "REPORT SCRIPT ERROR: " + scriptName + " : " + exc.getMessage();
			Msg.error(this, logErrorMsg, exc);
		}

		return retOption;
	}

	private GhidraState getInitialProgramState(Program program) {
		ProgramLocation location = null;
		AddressSetView initializedMem = program.getMemory().getLoadedAndInitializedAddressSet();
		if (!initializedMem.isEmpty()) {
			location = new ProgramLocation(program, initializedMem.getMinAddress());
		}
		return new GhidraState(null, project, program, location, null, null);
	}

	/**
	 *{@literal Run prescripts -> analysis -> postscripts (any of these steps is optional).}
	 * @param fileAbsolutePath Path of the file to analyze.
	 * @param program The program to analyze.
	 * @return true if the program file should be kept.  If analysis or scripts have marked
	 * 			the program as temporary changes should not be saved.  Returns false in
	 * 			these cases:
	 * 		- One of the scripts sets the Headless Continuation Option to "ABORT_AND_DELETE" or
	 * 			"CONTINUE_THEN_DELETE".
	 */
	private boolean analyzeProgram(String fileAbsolutePath, Program program) {

		analysisTimedOut = false;

		AutoAnalysisManager mgr = AutoAnalysisManager.getAnalysisManager(program);
		mgr.initializeOptions();

		GhidraState scriptState = null;
		HeadlessContinuationOption scriptStatus = HeadlessContinuationOption.CONTINUE;

		boolean abortProcessing = false;
		boolean deleteProgram = false;

		if (!options.preScripts.isEmpty()) {
			// create one state, in case each script might want to modify it to pass information
			scriptState = getInitialProgramState(program);

			scriptStatus = runScriptsList(options.preScripts, options.preScriptFileMap, scriptState,
				scriptStatus);
		}

		switch (scriptStatus) {
			case ABORT_AND_DELETE:
				abortProcessing = true;
				deleteProgram = true;
				break;

			case CONTINUE_THEN_DELETE:
				abortProcessing = false;
				deleteProgram = true;
				break;

			case ABORT:
				abortProcessing = true;
				deleteProgram = false;
				break;

			default:
				// do nothing
		}

		if (abortProcessing) {
			Msg.info(this, "Processing aborted as a result of pre-script.");
			mgr.dispose();
			return !deleteProgram;
		}

		int txId = program.startTransaction("Analysis");
		try {
			if (options.analyze) {
				Msg.info(this, "ANALYZING all memory and code: " + fileAbsolutePath);
				mgr.initializeOptions();

				// Note: Want to analyze regardless of whether we have already analyzed or not
				// (user could have changed options).
				mgr.reAnalyzeAll(null);

				if (options.perFileTimeout == -1) {
					mgr.startAnalysis(TaskMonitor.DUMMY); // kick start

					Msg.info(this, "REPORT: Analysis succeeded for file: " + fileAbsolutePath);
					GhidraProgramUtilities.markProgramAnalyzed(program);
				}
				else {
					HeadlessTimedTaskMonitor timerMonitor =
						new HeadlessTimedTaskMonitor(options.perFileTimeout);
					mgr.startAnalysis(timerMonitor);

					if (timerMonitor.isCancelled()) {
						Msg.error(this, "REPORT: Analysis timed out at " + options.perFileTimeout +
							" seconds. Processing not completed for file: " + fileAbsolutePath);

						// If no further scripts, just return the current program disposition
						if (options.postScripts.isEmpty()) {
							mgr.dispose();
							return !deleteProgram;
						}

						analysisTimedOut = true;
					}
					else {
						// If timeout didn't already happen at this point, cancel the monitor
						timerMonitor.cancel();

						Msg.info(this, "REPORT: Analysis succeeded for file: " + fileAbsolutePath);
						GhidraProgramUtilities.markProgramAnalyzed(program);
					}
				}
			}
		}
		finally {
			program.endTransaction(txId, true);
		}

		if (!options.postScripts.isEmpty()) {

			if (scriptState == null) {
				scriptState = getInitialProgramState(program);
			}

			scriptStatus = runScriptsList(options.postScripts, options.postScriptFileMap,
				scriptState, scriptStatus);

			switch (scriptStatus) {
				case ABORT_AND_DELETE:
					abortProcessing = true;
					deleteProgram = true;
					break;

				case CONTINUE_THEN_DELETE:
					abortProcessing = false;
					deleteProgram = true;
					break;

				case ABORT:
					abortProcessing = true;
					// If deleteProgram is already true, don't change it to false
					// (basically, leave as-is)
					break;

				default:
					// Do nothing, assume want to carry over options from before

			}

			if (abortProcessing) {
				Msg.info(this, "Processing aborted as a result of post-script.");
			}
			else if (options.analyze && !options.postScripts.isEmpty()) {
				Msg.info(this, "ANALYZING changes made by post scripts: " + fileAbsolutePath);
				txId = program.startTransaction("Post-Analysis");
				try {
					mgr.startAnalysis(TaskMonitor.DUMMY); // kick start
				}
				finally {
					program.endTransaction(txId, true);
				}
				Msg.info(this, "REPORT: Post-analysis succeeded for file: " + fileAbsolutePath);
			}

		}

		mgr.dispose();
		return !deleteProgram;
	}

	private void processFileNoImport(DomainFile domFile) throws IOException {

		if (domFile.isHijacked()) {
			Msg.error(this,
				"Skipped processing for " + domFile.getPathname() + " -- file is hijacked");
			return;
		}

		// Do not follow folder-links or consider program links.  Using content type
		// to filter is best way to control this.
		if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
			return; // skip non-Program files
		}

		Program program = null;
		boolean keepFile = true; // if false file should be deleted after release
		boolean terminateCheckoutWhenDone = false;

		boolean readOnlyFile =
			options.readOnly || domFile.isReadOnly() || !domFile.isInWritableProject();

		try {
			// Exclusive checkout required when commit option specified
			if (!readOnlyFile && domFile.isVersioned()) {
				if (!domFile.isCheckedOut()) {
					if (!domFile.canCheckout()) {
						Msg.warn(this, "Skipped processing for " + domFile.getPathname() +
							" within read-only repository");
						return;
					}
					if (!domFile.checkout(options.commit, TaskMonitor.DUMMY)) {
						Msg.warn(this, "Skipped processing for " + domFile.getPathname() +
							" -- failed to get exclusive file checkout required for commit");
						return;
					}
					// Only terminate checkout when done if we did the checkout
					terminateCheckoutWhenDone = true;
				}
				else if (options.commit && !domFile.isCheckedOutExclusive()) {
					Msg.error(this, "Skipped processing for " + domFile.getPathname() +
						" -- file is checked-out non-exclusive (commit requires exclusive checkout)");
					return;
				}
			}

			program = (Program) domFile.getDomainObject(this, true, false, TaskMonitor.DUMMY);

			String readOnlyText = readOnlyFile ? "read-only " : "";
			Msg.info(this,
				"REPORT: Processing " + readOnlyText + "project file: " + domFile.getPathname());

			// This method already takes into account whether the user has set the "noanalysis"
			// flag or not
			keepFile = analyzeProgram(domFile.getPathname(), program) || readOnlyFile;

			if (!keepFile) {
				program.setTemporary(true); // don't save changes
				if (!options.okToDelete) {
					// Don't remove file unless okToDelete was specified
					Msg.warn(this, "Due to script activity, " + domFile.getPathname() +
						" deletion was requested but denied -- 'okToDelete' parameter was not specified");
					keepFile = true;
				}
			}

			if (readOnlyFile) {
				if (program.isChanged()) {
					Msg.info(this, "REPORT: Discarding changes to the following read-only file: " +
						domFile.getPathname());
				}
				return;
			}

			if (program.isTemporary()) {
				if (program.isChanged()) {
					Msg.info(this,
						"REPORT: Discarding changes to the following file as a result of script activity: " +
							domFile.getPathname());
				}
				return;
			}

			if (domFile.canSave()) {
				domFile.save(TaskMonitor.DUMMY);
				Msg.info(this,
					"REPORT: Save succeeded for processed file: " + domFile.getPathname());
			}
			if (program.isChanged()) {
				Msg.error(this,
					"REPORT: Error trying to save changes to file: " + domFile.getPathname());
			}

			if (options.commit) {

				program.release(this);
				program = null;

				// Only commit if it's a shared project.
				commit(domFile);
			}
		}
		catch (VersionException e) {

			if (e.isUpgradable()) {
				Msg.error(this,
					domFile.getPathname() +
						": this file was created with an older version of Ghidra.  Automatic " +
						"upgrading of the file to the current version is possible, but " +
						"requires an exclusive check-out of the file.  Please check out the file " +
						" using the Ghidra GUI and then re-run Headless.");
			}
			else {
				Msg.error(this, domFile.getPathname() +
					": this file was created with a newer version of Ghidra, and can not be processed.");
			}
		}
		catch (CancelledException e) {
			// This can never happen because there is no user interaction in headless!
		}
		catch (Exception exc) {
			Msg.error(this, domFile.getPathname() + " Error during analysis: " + exc.getMessage(),
				exc);
		}
		finally {

			if (program != null) {
				program.release(this);
				program = null;
			}

			if (!readOnlyFile) { // can't change anything if read-only file

				// Undo checkout of it is still checked-out and either the file is to be
				// deleted, or we just checked it out and file changes have been committed
				if (domFile.isCheckedOut()) {
					if (!keepFile ||
						(terminateCheckoutWhenDone && !domFile.modifiedSinceCheckout())) {
						domFile.undoCheckout(false);
					}
				}

				if (!keepFile) {
					deleteDomainFile(domFile);
				}
			}
		}
	}

	private void deleteDomainFile(DomainFile domFile) {
		if (domFile.isCheckedOut()) {
			Msg.error(this, "Failed to delete file as requested due to pre-existing checkout: " +
				domFile.getPathname());
			return;
		}

		try {
			domFile.delete();
		}
		catch (IOException e) {
			Msg.error(this, "Failed to delete file as requested - " + e.getMessage() + ": " +
				domFile.getPathname());
		}
	}

	/**
	 * Process all files within parentFolder which satisfies the specified filenamePattern.
	 * If filenamePattern is null, all files will be processed
	 * @param parentFolder domain folder to be searched
	 * @param filenamePattern filename pattern or null for all files
	 * @return true if one or more files processed
	 * @throws IOException if an IO problem occurred.
	 */
	private boolean processFolderNoImport(DomainFolder parentFolder, Pattern filenamePattern)
			throws IOException {

		if (parentFolder.isEmpty()) {
			return false;
		}

		boolean filesProcessed = false;

		for (DomainFile domFile : parentFolder.getFiles()) {
			if (filenamePattern == null || filenamePattern.matcher(domFile.getName()).matches()) {
				// Do not follow folder-links or consider program links.  Using content type
				// to filter is best way to control this.
				if (ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
					filesProcessed = true;
					processFileNoImport(domFile);
				}
			}
		}

		if (options.recursive) {
			for (DomainFolder folder : parentFolder.getFolders()) {
				filesProcessed |= processFolderNoImport(folder, filenamePattern);
			}
		}

		return filesProcessed;
	}

	/**
	 * Process the specified filename within parentFolder.
	 * @param parentFolder domain folder to be searched
	 * @param filename name of file to be imported
	 * @return true if one or more files processed
	 * @throws IOException if an IO problem occurred.
	 */
	private boolean processFolderNoImport(DomainFolder parentFolder, String filename)
			throws IOException {

		if (parentFolder.isEmpty()) {
			return false;
		}

		boolean filesProcessed = false;

		DomainFile domFile = parentFolder.getFile(filename);
		// Do not follow folder-links or program links.  Using content type
		// to filter is best way to control this.
		if (domFile != null &&
			ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
			filesProcessed = true;
			processFileNoImport(domFile);
		}

		if (options.recursive) {
			for (DomainFolder folder : parentFolder.getFolders()) {
				filesProcessed |= processFolderNoImport(folder, filename);
			}
		}

		return filesProcessed;
	}

	private void processNoImport(String rootFolderPath) throws IOException {

		storage.clear();

		DomainFolder domFolder = project.getProjectData().getFolder(rootFolderPath);
		if (domFolder == null) {
			throw new IOException("Specified project folder not found: " + rootFolderPath);
		}

		Pattern filenamePattern = null;
		if (options.domainFileNameToProcess != null) {
			filenamePattern = createFilenamePattern(options.domainFileNameToProcess);
		}

		boolean filesProcessed = false;
		if (filenamePattern == null && options.domainFileNameToProcess != null) {
			// assume domainFileNameToProcess was a specific filename and not a pattern
			filesProcessed = processFolderNoImport(domFolder, options.domainFileNameToProcess);
		}
		else {
			filesProcessed = processFolderNoImport(domFolder, filenamePattern);
		}

		if (!filesProcessed) {
			if (options.domainFileNameToProcess != null) {
				throw new IOException("Requested project program file(s) not found: " +
					options.domainFileNameToProcess);
			}
			throw new IOException("No program files found within specified project folder: " +
				domFolder.getPathname());
		}
	}

	private Pattern createFilenamePattern(String name) {

		if ((name.indexOf('*') == -1) && (name.indexOf('?') == -1)) {
			// not a 'search' pattern
			return null;
		}

		// If surrounded by single-quotes, strip them, as to not interfere with the Pattern
		if ((name.startsWith("\'")) && (name.endsWith("\'"))) {
			name = name.substring(1, name.length() - 1);
		}

		// Find files that match the wildcard pattern
		Pattern p = UserSearchUtils.createSearchPattern(name, true);
		return p;
	}

	private boolean checkOverwrite(Loaded<? extends DomainObject> loaded) throws IOException {
		DomainFolder folder = project.getProjectData().getFolder(loaded.getProjectFolderPath());
		if (folder == null) {
			return true;
		}
		DomainFile df = folder.getFile(loaded.getName());
		if (df == null) {
			return true;
		}
		if (options.overwrite) {
			try {
				if (df.isHijacked()) {
					Msg.error(this,
						"REPORT: Found conflicting program file in project which is hijacked - overwrite denied: " +
							df.getPathname());
					return false;
				}
				if (df.isVersioned()) {
					if (!options.commit) {
						Msg.error(this,
							"REPORT: Found conflicting versioned program file in project with changes - overwrite denied when commit disabled: " +
								df.getPathname());
						return false;
					}
					if (df.isCheckedOut()) {
						df.undoCheckout(false);
					}
				}
				try {
					df.delete();
				}
				catch (IOException e) {
					Msg.error(this, "REPORT: Failed to remove conflicting program file (" +
						e.getMessage() + "): " + df.getPathname());
					return false;
				}
			}
			catch (UserAccessException e) {
				Msg.error(this,
					"REPORT: Found conflicting program file in project which user is unable to overwrite: " +
						df.getPathname());
				return false;
			}
			Msg.warn(this,
				"REPORT: Removed conflicting program file from project: " + df.getPathname());
		}
		else {
			Msg.error(this,
				"REPORT: Found conflicting program file in project: " + df.getPathname());
			return false;
		}
		return true;
	}

	private void commit(DomainFile df) throws IOException {

		RepositoryAdapter rep = project.getRepository();
		if (rep != null) {
			try {
				rep.connect();
			}
			catch (IOException e) {
				ClientUtil.handleException(rep, e, "Connect", null);
			}
			if (!rep.isConnected()) {
				Msg.error(this,
					df.getPathname() + ": File check-in failed - repository connection error");
				throw new IOException(
					df.getPathname() + ": File check-in failed - repository connection error");
			}
		}

		if (df.canAddToRepository()) {
			try {
				df.addToVersionControl(options.commitComment, false, TaskMonitor.DUMMY);
				Msg.info(this, "REPORT: Added file to repository: " + df.getPathname());
			}
			catch (IOException e) {
				Msg.error(this, df.getPathname() + ": File check-in failed - " + e.getMessage());
				throw e;
			}
			catch (CancelledException e) {
				// this can never happen because there is no user interaction in headless!
			}
		}
		else if (df.canCheckin()) {
			try {
				df.checkin(new CheckinHandler() {
					@Override
					public boolean keepCheckedOut() throws CancelledException {
						return true;
					}

					@Override
					public String getComment() throws CancelledException {
						return options.commitComment;
					}

					@Override
					public boolean createKeepFile() throws CancelledException {
						return false;
					}
				}, TaskMonitor.DUMMY);
				Msg.info(this, "REPORT: Committed file changes to repository: " + df.getPathname());
			}
			catch (IOException e) {
				Msg.error(this, df.getPathname() + ": File check-in failed - " + e.getMessage());
				throw e;
			}
			catch (VersionException e) {
				Msg.error(this,
					df.getPathname() + ": File check-in failed - version error occurred");
			}
			catch (CancelledException e) {
				// this can never happen because there is no user interaction in headless!
			}
		}
		else {
			Msg.error(this, df.getPathname() + ": Unable to commit file");
		}
	}

	private boolean processFileWithImport(FSRL fsrl, String folderPath) {

		Msg.info(this, "IMPORTING: " + fsrl);

		// Perform the load.
		// Note that loading 1 file may result in more than 1 thing getting loaded.
		LoadResults<? extends DomainObject> loadResults = null;
		try {
			loadResults = ProgramLoader.builder()
					.source(fsrl)
					.project(project)
					.projectFolderPath(folderPath)
					.mirror(options.mirror)
					.language(options.language)
					.compiler(options.compilerSpec)
					.loaders(options.loaderClass)
					.loaderArgs(options.loaderArgs)
					.loadAll();

			Msg.info(this, "IMPORTING: Loaded " + (loadResults.size() - 1) + " additional files");

			// Make sure we are allowed to save ALL domain objects to the project.
			// If not, save none and fail.
			if (!options.readOnly) {
				for (Loaded<? extends DomainObject> loaded : loadResults) {
					if (!checkOverwrite(loaded)) {
						return false;
					}
				}
			}

			boolean doSave = !options.readOnly;
			Loaded<? extends DomainObject> primary = loadResults.getPrimary();
			DomainObject primaryDomainObject = primary.getDomainObject(this);
			try {
				if (primaryDomainObject instanceof Program primaryProgram) {
					// Check if there are defined memory blocks in the primary program.
					// Abort if not (there is nothing to work with!).
					if (primaryProgram.getMemory().getAllInitializedAddressSet().isEmpty()) {
						Msg.error(this,
							"REPORT: Error: No memory blocks were defined for file " + fsrl);
						return false;
					}

					// Analyze the primary program, and determine if we should save.
					// TODO: Analyze non-primary programs (GP-2965).
					doSave = analyzeProgram(fsrl.toString(), primaryProgram) && doSave;
				}
			}
			finally {
				primaryDomainObject.release(this);
			}

			// The act of marking the program as temporary by a script will signal
			// us to discard any changes
			if (!doSave) {
				loadResults.forEach(e -> e.apply(p -> p.setTemporary(true)));
			}

			// Apply saveDomainFolder to the primary program, if applicable.
			// We don't support changing the save folder on any non-primary loaded programs.
			// Note that saveDomainFolder is set by pre/post-scripts, so it can only be used
			// after analysis happens.
			if (saveDomainFolder != null) {
				primary.setProjectFolderPath(saveDomainFolder.getPathname());
				if (!checkOverwrite(primary)) {
					return false;
				}
			}

			// Save
			for (Loaded<? extends DomainObject> loaded : loadResults) {
				if (!loaded.check(DomainObject::isTemporary)) {
					try {
						DomainFile domainFile = loaded.save(TaskMonitor.DUMMY);
						Msg.info(this, String.format("REPORT: Save succeeded for: %s (%s)", loaded,
							domainFile));
					}
					catch (IOException e) {
						Msg.info(this, "REPORT: Save failed for: " + loaded);
					}
				}
				else {
					if (options.readOnly) {
						Msg.info(this,
							"REPORT: Discarded file import due to readOnly option: " + loaded);
					}
					else {
						Msg.info(this, "REPORT: Discarded file import as a result of script " +
							"activity or analysis timeout: " + loaded);
					}
				}
			}

			// Commit changes
			if (options.commit) {
				for (Loaded<? extends DomainObject> loaded : loadResults) {
					if (!loaded.check(DomainObject::isTemporary)) {
						loaded.close(); // we need to close before committing
						commit(loaded.getSavedDomainFile());
					}
				}
			}

			Msg.info(this, "REPORT: Import succeeded");
			return true;
		}
		catch (LoadException e) {
			Msg.error(this, "The ProgramLoader could not successfully load " + fsrl +
				" with the provided import parameters. Please ensure that any specified" +
				" processor/cspec arguments are compatible with the loader that is used during" +
				" import and try again.");
			if (options.loaderClass != null && options.loaderClass != BinaryLoader.class) {
				Msg.error(this,
					"NOTE: Import failure may be due to missing opinion for \"" +
						options.loaderClass.getSimpleName() +
						"\". If so, please contact Ghidra team for assistance.");
			}
			return false;
		}
		catch (Exception e) {
			Msg.error(this, "REPORT: " + e.getMessage(), e);
			return false;
		}
		finally {
			if (loadResults != null) {
				loadResults.close();
			}
		}
	}

	private void processWithImport(FSRL fsrl, String folderPath, Integer depth, boolean isFirstTime)
			throws IOException {
		try (RefdFile refdFile = fsService.getRefdFile(fsrl, TaskMonitor.DUMMY)) {
			GFile file = refdFile.file;
			if (depth == null && isFirstTime) {
				depth = file.isDirectory() ? 0 : 1; // set default depth
			}
			if ((options.recursive || isFirstTime) && file.isDirectory()) {
				processFS(file.getFilesystem(), file, folderPath, depth);
				return;
			}
			if (options.recursive && depth > 0 && processAsFS(fsrl, folderPath, depth)) {
				return;
			}
			if (!file.isDirectory() && processWithLoader(fsrl, folderPath)) {
				return;
			}
		}
		catch (CancelledException e) {
			Msg.info(this, "REPORT: Importing cancelled");
		}
	}

	private void processFS(GFileSystem fs, GFile startDir, String folderPath, int depth)
			throws CancelledException, IOException {
		if (!folderPath.endsWith(DomainFolder.SEPARATOR)) {
			folderPath += DomainFolder.SEPARATOR;
		}
		folderPath += startDir.getName();

		for (GFile file : fs.getListing(startDir)) {
			String name = file.getName();
			if (name.startsWith(".")) {
				Msg.warn(this, "Ignoring file '" + name + "'.");
				continue;
			}
			FSRL fqFSRL;
			try {
				fqFSRL = fsService.getFullyQualifiedFSRL(file.getFSRL(), TaskMonitor.DUMMY);
			}
			catch (IOException e) {
				Msg.warn(this, "Error getting info for " + file.getFSRL());
				continue;
			}
			try {
				checkValidFilename(fqFSRL.getName());
				processWithImport(fqFSRL, folderPath, depth, false);
			}
			catch (InvalidInputException e) {
				// Just move on if not valid
			}
		}
	}

	private boolean processAsFS(FSRL fsrl, String folderPath, int depth) throws CancelledException {
		try (FileSystemRef fsRef = fsService.probeFileForFilesystem(fsrl, TaskMonitor.DUMMY,
			FileSystemProbeConflictResolver.CHOOSEFIRST)) {
			if (fsRef == null) {
				return false;
			}
			if (!folderPath.endsWith(DomainFolder.SEPARATOR)) {
				folderPath += DomainFolder.SEPARATOR;
			}
			folderPath += fsrl.getName();
			processWithImport(fsRef.getFilesystem().getFSRL(), folderPath, depth - 1, false);
			return true;
		}
		catch (IOException e) {
			return false;
		}
	}

	private boolean processWithLoader(FSRL fsrl, String folderPath) {
		boolean importSucceeded = processFileWithImport(fsrl, folderPath);

		// Check to see if there are transient programs lying around due
		// to programs not being released during Importing
		List<DomainFile> domainFileContainer = new ArrayList<>();
		TransientDataManager.getTransients(domainFileContainer);
		if (domainFileContainer.size() > 0) {
			TransientDataManager.releaseFiles(this);
		}

		if (!importSucceeded) {
			Msg.error(this, "REPORT: Import failed for file: " + fsrl);
		}
		return importSucceeded;
	}

	private void processWithImport(String folderPath, List<File> inputDirFiles) throws IOException {

		storage.clear();

		if (inputDirFiles != null && !inputDirFiles.isEmpty()) {
			Msg.info(this, "REPORT: Processing input files: ");
			Msg.info(this, "     project: " + project.getProjectLocator());
			List<FSRL> fsrls = inputDirFiles.stream().map(f -> fsService.getLocalFSRL(f)).toList();
			for (FSRL fsrl : fsrls) {
				processWithImport(fsrl, folderPath, options.recursiveDepth, true);
			}
		}
		else {
			//no input, just run the scripts

			//create one state, in case each script might want to modify it to pass information
			GhidraState scriptState = new GhidraState(null, project, null, null, null, null);

			HeadlessContinuationOption scriptStatus = HeadlessContinuationOption.CONTINUE;

			scriptStatus = runScriptsList(options.preScripts, options.preScriptFileMap, scriptState,
				scriptStatus);

			// Since there is no program, "DELETE" is meaningless here.
			// If status asks for ABORT, then don't continue running the postscript.
			switch (scriptStatus) {
				case ABORT:
				case ABORT_AND_DELETE:
					return;

				default:
					// Just continue
			}

			runScriptsList(options.postScripts, options.postScriptFileMap, scriptState,
				scriptStatus);
		}
	}

	private Project openProject(ProjectLocator locator) throws IOException {
		Project tempProject;

		if (options.deleteProject) {
			Msg.warn(this, "Project already exists and will not be deleted: " + locator);
			options.deleteProject = false;
		}

		Msg.info(this, "Opening existing project: " + locator);
		try {
			tempProject = new HeadlessProject(getProjectManager(), locator);
		}
		catch (NotFoundException | NotOwnerException | LockException e) {
			throw new IOException(e);
		}

		return tempProject;

	}

	/**
	 * Checks to make sure the given file contains only valid characters in its name.
	 * 
	 * @param path The path of the file to check.
	 * @throws InvalidInputException if the given file path contains invalid characters in it.
	 */
	static void checkValidFilename(String path) throws InvalidInputException {
		String filename = FilenameUtils.getName(path);

		for (int i = 0; i < filename.length(); i++) {
			char c = filename.charAt(i);
			if (!LocalFileSystem.isValidNameCharacter(c)) {
				throw new InvalidInputException(
					"'" + filename + "' contains the invalid character: \'" + c +
						"\' and can not be imported (full path: " + path + "). Please rename.");
			}
		}
	}

	private HeadlessGhidraProjectManager getProjectManager() {
		if (projectManager == null) {
			projectManager = new HeadlessGhidraProjectManager();
		}
		return projectManager;
	}

	/**
	 * Ghidra project class required to gain access to specialized project constructor
	 * for URL connection.
	 */
	private static class HeadlessProject extends DefaultProject {

		HeadlessProject(HeadlessGhidraProjectManager projectManager, ProjectLocator projectLocator)
				throws NotFoundException, NotOwnerException, LockException, IOException {
			super(projectManager, projectLocator, false);
			AppInfo.setActiveProject(this);
		}

		HeadlessProject(HeadlessGhidraProjectManager projectManager, ProjectData projectData) {
			super(projectManager, (DefaultProjectData) projectData);
			AppInfo.setActiveProject(this);
		}
	}

	/**
	 * A headless version of the {@link DefaultProjectManager} that does not update the project's 
	 * preferences. This prevents the headless environment from overwriting settings GUI 
	 * installations.
	 */
	private static class HeadlessGhidraProjectManager extends DefaultProjectManager {

		@Override
		public void setLastOpenedProject(ProjectLocator projectLocator) {
			// No need to save this for headless.  We also do not want to affect the GUI by saving
			// this value.
		}

		@Override
		public ProjectLocator getLastOpenedProject() {
			return null;
		}

		@Override
		protected void updatePreferences() {
			// nothing to save
		}
	}
}
