GP-3697 Added delayed ProjectFileManager disposal in support of URL use

and opening linked project files and renamed ProjectFileData to
DefaultProjectData.

Ghidra/Debug/Debugger/src/main/java/ghidra/app/plugin/core/debug/DebuggerCoordinates.java

@@ -23,7 +23,7 @@ import org.jdom.Element;
 import ghidra.app.services.DebuggerTraceManagerService;
 import ghidra.app.services.TraceRecorder;
 import ghidra.dbg.target.TargetObject;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.*;
 import ghidra.framework.options.SaveState;
 import ghidra.framework.plugintool.PluginTool;
@@ -664,7 +664,7 @@ public class DebuggerCoordinates {
 		if (projData == null) {
 			try {
 				// FIXME! orphaned instance - transient in nature
-				projData = new ProjectFileManager(projLoc, false, false);
+				projData = new DefaultProjectData(projLoc, false, false);
 			}
 			catch (NotOwnerException e) {
 				Msg.showError(DebuggerCoordinates.class, tool.getToolFrame(), "Trace Open Failed",

Ghidra/Debug/Debugger/src/main/java/ghidra/app/plugin/core/debug/gui/model/ObjectTreeModel.java

@@ -25,6 +25,7 @@ import docking.widgets.tree.GTreeNode;
 import ghidra.app.plugin.core.debug.gui.DebuggerResources;
 import ghidra.dbg.target.*;
 import ghidra.dbg.util.PathUtils.TargetObjectKeyComparator;
+import ghidra.framework.model.DomainObject;
 import ghidra.framework.model.DomainObjectClosedListener;
 import ghidra.trace.model.*;
 import ghidra.trace.model.Trace.TraceObjectChangeType;
@@ -45,7 +46,7 @@ public class ObjectTreeModel implements DisplaysModified {
 		}
 
 		@Override
-		public void domainObjectClosed() {
+		public void domainObjectClosed(DomainObject dobj) {
 			setTrace(null);
 		}
 

Ghidra/Debug/Debugger/src/main/java/ghidra/app/plugin/core/debug/service/modules/ProgramModuleIndexer.java

@@ -94,7 +94,8 @@ public class ProgramModuleIndexer implements DomainFolderChangeAdapter {
 		}
 
 		@Override
-		public void domainObjectClosed() {
+		public void domainObjectClosed(DomainObject dobj) {
+			// assume dobj == program
 			dispose();
 		}
 
@@ -353,9 +354,8 @@ public class ProgramModuleIndexer implements DomainFolderChangeAdapter {
 		 * trace, or bogus external libraries in a mapped program, scoring libraries before module
 		 * names should not cause problems.
 		 */
-		Comparator<IndexEntry> comparator = byIsLibrary
-				.thenComparing(byNameSource)
-				.thenComparing(byFolderUses);
+		Comparator<IndexEntry> comparator =
+			byIsLibrary.thenComparing(byNameSource).thenComparing(byFolderUses);
 		return projectData.getFileByID(entries.stream().max(comparator).get().dfID);
 	}
 

Ghidra/Features/Base/developer_scripts/CleanupMergeDatabasesScript.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -14,16 +13,16 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
+import java.io.IOException;
+import java.lang.reflect.Method;
+
 import ghidra.app.script.GhidraScript;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.Project;
 import ghidra.framework.store.FileSystem;
 import ghidra.framework.store.local.LocalFileSystem;
 import ghidra.framework.store.local.LocalFolderItem;
 
-import java.io.IOException;
-import java.lang.reflect.Method;
-
 public class CleanupMergeDatabasesScript extends GhidraScript {
 
 	@Override
@@ -31,8 +30,8 @@ public class CleanupMergeDatabasesScript extends GhidraScript {
 
 		Project project = state.getProject();
 
-		ProjectFileManager fileMgr = (ProjectFileManager) project.getProjectData();
-		LocalFileSystem fs = (LocalFileSystem) fileMgr.getPrivateFileSystem();
+		DefaultProjectData projectData = (DefaultProjectData) project.getProjectData();
+		LocalFileSystem fs = (LocalFileSystem) projectData.getPrivateFileSystem();
 
 		int cnt = cleanupFolder(fs, "/");
 
@@ -61,9 +60,8 @@ public class CleanupMergeDatabasesScript extends GhidraScript {
 		}
 
 		// fs.getItemNames(folderPath, true)
-		String[] itemNames =
-			(String[]) invokeInstanceMethod("getItemNames", fs, new Class[] { String.class,
-				boolean.class }, new Object[] { folderPath, true });
+		String[] itemNames = (String[]) invokeInstanceMethod("getItemNames", fs,
+			new Class[] { String.class, boolean.class }, new Object[] { folderPath, true });
 
 		for (String itemName : itemNames) {
 			if (!itemName.startsWith(LocalFileSystem.HIDDEN_ITEM_PREFIX)) {
@@ -78,8 +76,9 @@ public class CleanupMergeDatabasesScript extends GhidraScript {
 			else {
 				// make sure we get item out of index
 				//fs.deallocateItemStorage(folderPath, itemName);
-				invokeInstanceMethod("deallocateItemStorage", fs, new Class[] { String.class,
-					String.class }, new Object[] { folderPath, itemName });
+				invokeInstanceMethod("deallocateItemStorage", fs,
+					new Class[] { String.class, String.class },
+					new Object[] { folderPath, itemName });
 			}
 			++cnt;
 		}

Ghidra/Features/Base/ghidra_scripts/AskScript.java

@@ -75,7 +75,16 @@ public class AskScript extends GhidraScript {
 			}
 
 			Program prog = askProgram("Please choose a program to open.");
+			if (prog != null) {
+				// NOTE: if prog is not null script must release it when done using.
+				// This may also be accomplished via an overridden cleanup(boolean) method.
+				try {
 					println("Program picked: " + prog.getName());
+				}
+				finally {
+					prog.release(this); // will remain open in tool if applicable
+				}
+			}
 
 			DomainFile domFile = askDomainFile("Which domain file would you like?");
 			println("Domain file: " + domFile.getName());

Ghidra/Features/Base/ghidra_scripts/CompareAnalysisScript.java

@@ -38,6 +38,7 @@ public class CompareAnalysisScript extends GhidraScript {
 		if (otherProgram == null) {
 			return;
 		}
+		try {
 			println("\n\n****** COMPARING FUNCTIONS:\n");
 			compareFunctions(otherProgram);
 			println("\n\n****** COMPARING STRINGS:\n");
@@ -52,6 +53,10 @@ public class CompareAnalysisScript extends GhidraScript {
 			println("\n\n****** COMPARING ERRORS:\n");
 			compareErrors(otherProgram);
 		}
+		finally {
+			otherProgram.release(this);
+		}
+	}
 
 	void compareFunctions(Program otherProgram) {
 		FunctionManager functionManager = otherProgram.getFunctionManager();

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/analysis/AnalysisStateInfo.java

@@ -73,7 +73,7 @@ public class AnalysisStateInfo {
 		if (stateMap == null) {
 			stateMap = new HashMap<>();
 			programStates.put(program, stateMap);
-			program.addCloseListener(() -> programStates.remove(program));
+			program.addCloseListener(doa -> programStates.remove(program));
 		}
 		stateMap.put(state.getClass(), state);
 	}

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/analysis/AutoAnalysisManager.java

@@ -57,7 +57,7 @@ import ghidra.util.task.*;
  * Provides support for auto analysis tasks.
  * Manages a pipeline or priority of tasks to run given some event has occurred.
  */
-public class AutoAnalysisManager implements DomainObjectListener, DomainObjectClosedListener {
+public class AutoAnalysisManager implements DomainObjectListener {
 
 	/**
 	 * The name of the shared thread pool that analyzers can uses to do parallel processing.
@@ -145,7 +145,7 @@ public class AutoAnalysisManager implements DomainObjectListener, DomainObjectCl
 	private AutoAnalysisManager(Program program) {
 		this.program = program;
 		eventQueueID = program.createPrivateEventQueue(this, 500);
-		program.addCloseListener(this);
+		program.addCloseListener(dobj -> dispose());
 		initializeAnalyzers();
 	}
 
@@ -361,11 +361,6 @@ public class AutoAnalysisManager implements DomainObjectListener, DomainObjectCl
 			subType == ChangeManager.FUNCTION_CHANGED_RETURN;
 	}
 
-	@Override
-	public void domainObjectClosed() {
-		dispose();
-	}
-
 	@Override
 	public void domainObjectChanged(DomainObjectChangedEvent ev) {
 		if (program == null) {
@@ -961,10 +956,7 @@ public class AutoAnalysisManager implements DomainObjectListener, DomainObjectCl
 		}
 
 		PluginTool anyTool = null;
-		Iterator<PluginTool> iterator = toolSet.iterator();
-		while (iterator.hasNext()) {
-			PluginTool tool = iterator.next();
-
+		for (PluginTool tool : toolSet) {
 			anyTool = tool;
 			JFrame toolFrame = tool.getToolFrame();
 			if (toolFrame != null && toolFrame.isActive()) {

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/marker/MarkerManager.java

@@ -33,7 +33,6 @@ import ghidra.app.nav.Navigatable;
 import ghidra.app.services.*;
 import ghidra.app.util.viewer.listingpanel.*;
 import ghidra.app.util.viewer.util.AddressIndexMap;
-import ghidra.framework.model.DomainObjectClosedListener;
 import ghidra.framework.plugintool.Plugin;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.program.model.address.Address;
@@ -510,30 +509,19 @@ public class MarkerManager implements MarkerService {
 		private final AddressColorCache colorCache = new AddressColorCache();
 		private final ColorBlender blender = new ColorBlender();
 
-		private final MarkerSetCache cache;
-		private final Program program;
-		private final DomainObjectClosedListener closeListener = this::programClosed;
-
 		public MarkerSetCacheEntry(MarkerSetCache cache, Program program) {
-			this.cache = cache;
-			this.program = program;
 			/**
 			 * Use this close listener approach instead of plugin events, since we don't get a
 			 * ProgramClosedPluginEvent when a trace view is closed, but we can listen for its
 			 * domain object closing, which works for plain programs, too.
 			 */
-			program.addCloseListener(closeListener);
+			program.addCloseListener(dobj -> cache.programClosed(program));
 		}
 
 		void clearColors() {
 			colorCache.clear();
 		}
 
-		private void programClosed() {
-			program.removeCloseListener(closeListener);
-			cache.programClosed(program);
-		}
-
 		MarkerSetImpl getByName(String name) {
 			for (MarkerSetImpl set : markerSets) {
 				if (name.equals(set.getName())) {

Ghidra/Features/Base/src/main/java/ghidra/app/script/GhidraScript.java

@@ -1883,6 +1883,9 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	 * @param transformer the function to turn a String into a T
 	 * @param key the values used to create a key for lookup in the script properties file
 	 * @return null if no value was found in the aforementioned sources
+	 * @throws IllegalArgumentException if the loaded String value cannot be parsed into a
+	 *                                  <code>T</code> or property not defined when in headless
+	 *                                  mode.
 	 */
 	private <T> T loadAskValue(StringTransformer<T> transformer, String key) {
 		T value = loadAskValue(null, transformer, key);
@@ -1897,11 +1900,12 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	 * @param defaultValue an optional default value that will be used if no suitable
 	 *                     value can be found in script args or a properties file
 	 * @param transformer the function to turn a String into a T
-	 * @param key the values used to create a key for lookup in the script properties file
+	 * @param key the value property key used for lookup in the script properties file
 	 * @return null if no value was found in the aforementioned sources
 	 *
 	 * @throws IllegalArgumentException if the loaded String value cannot be parsed into a
-	 *                                  <code>T</code>.
+	 *                                  <code>T</code> or property not defined when in headless
+	 *                                  mode and no defaultValue has been specified.
 	 */
 	private <T> T loadAskValue(T defaultValue, StringTransformer<T> transformer, String key) {
 
@@ -2550,7 +2554,8 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	 * @throws IllegalArgumentException if in headless mode, there was a missing or invalid Address
 	 * 			specified in the .properties file
 	 */
-	public Address askAddress(String title, String message, String defaultValue) throws CancelledException {
+	public Address askAddress(String title, String message, String defaultValue)
+			throws CancelledException {
 
 		String key = join(title, message);
 
@@ -2683,7 +2688,12 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	 *
 	 * @param title the title of the pop-up dialog (in GUI mode) or the variable name (in
 	 * 			headless mode)
-	 * @return the user-specified Program
+	 * @return the user-selected Program with this script as the consumer or null if a program was 
+	 * not selected.  NOTE: It is very important that the program instance returned by this method 
+	 * ALWAYS be properly released when no longer needed.  The script which invoked this method must be
+	 * specified as the consumer upon release (i.e., {@code program.release(this) } - failure to 
+	 * properly release the program may result in improper project disposal.  If the program was 
+	 * opened by the tool, the tool will be a second consumer responsible for its own release.
 	 * @throws VersionException if the Program is out-of-date from the version of GHIDRA
 	 * @throws IOException if there is an error accessing the Program's DomainObject
 	 * @throws CancelledException if the operation is cancelled
@@ -2693,12 +2703,9 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	public Program askProgram(String title)
 			throws VersionException, IOException, CancelledException {
 
-		DomainFile existingValue = loadAskValue(this::parseDomainFile, title);
-		if (isRunningHeadless()) {
-			return (Program) existingValue.getDomainObject(this, false, false, monitor);
-		}
-
-		DomainFile choice = doAsk(Program.class, title, "", existingValue, lastValue -> {
+		DomainFile choice = loadAskValue(this::parseDomainFile, title);
+		if (!isRunningHeadless()) {
+			choice = doAsk(Program.class, title, "", choice, lastValue -> {
 
 				DataTreeDialog dtd = new DataTreeDialog(null, title, DataTreeDialog.OPEN);
 				dtd.show();
@@ -2708,18 +2715,22 @@ public abstract class GhidraScript extends FlatProgramAPI {
 
 				return dtd.getDomainFile();
 			});
+		}
 
 		if (choice == null) {
 			return null;
 		}
 
+		Program p = (Program) choice.getDomainObject(this, false, false, monitor);
+
 		PluginTool tool = state.getTool();
 		if (tool == null) {
-			return (Program) choice.getDomainObject(this, false, false, monitor);
+			return p;
 		}
 
 		ProgramManager pm = tool.getService(ProgramManager.class);
-		return pm.openProgram(choice);
+		pm.openProgram(p);
+		return p;
 	}
 
 	/**
@@ -2768,10 +2779,10 @@ public abstract class GhidraScript extends FlatProgramAPI {
 	 *
 	 * @param title the title of the pop-up dialog (in GUI mode) or the variable name (in headless
 	 * 		mode or when using .properties file)
-	 * @throws IllegalArgumentException if in headless mode, there was a missing or invalid	domain
-	 * 			file specified in the .properties file
 	 * @return the user-selected domain file
 	 * @throws CancelledException if the operation is cancelled
+	 * @throws IllegalArgumentException if in headless mode, there was a missing or invalid	domain
+	 * 			file specified in the .properties file
 	 */
 	public DomainFile askDomainFile(String title) throws CancelledException {
 
@@ -3015,8 +3026,7 @@ public abstract class GhidraScript extends FlatProgramAPI {
 			throw new ImproperUseException(
 				"The askPassword() method can only be used when running headed Ghidra.");
 		}
-		PasswordDialog dialog =
-			new PasswordDialog(title, null, null, prompt, null, null);
+		PasswordDialog dialog = new PasswordDialog(title, null, null, prompt, null, null);
 		try {
 			state.getTool().showDialog(dialog);
 			if (!dialog.okWasPressed()) {

Ghidra/Features/Base/src/main/java/ghidra/app/util/headless/HeadlessAnalyzer.java

@@ -1575,12 +1575,11 @@ public class HeadlessAnalyzer {
 				}
 				else {
 					if (options.readOnly) {
-						Msg.info(this, "REPORT: Discarded file import due to readOnly option: " +
-							loaded);
+						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 " +
+						Msg.info(this, "REPORT: Discarded file import as a result of script " +
 							"activity or analysis timeout: " + loaded);
 					}
 				}
@@ -1627,9 +1626,9 @@ public class HeadlessAnalyzer {
 		}
 	}
 
-	private LoadResults<Program> loadPrograms(File file, String folderPath) throws VersionException,
-			InvalidNameException, DuplicateNameException, CancelledException, IOException,
-			LoadException {
+	private LoadResults<Program> loadPrograms(File file, String folderPath)
+			throws VersionException, InvalidNameException, DuplicateNameException,
+			CancelledException, IOException, LoadException {
 		MessageLog messageLog = new MessageLog();
 
 		if (options.loaderClass == null) {

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/data/DefaultProjectDataTest.java

@@ -28,6 +28,7 @@ import org.junit.*;
 
 import generic.test.TestUtils;
 import ghidra.framework.model.*;
+import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.store.FileSystem;
 import ghidra.framework.store.FileSystemEventManager;
 import ghidra.framework.store.local.LocalFileSystem;
@@ -37,13 +38,13 @@ import ghidra.program.model.listing.Program;
 import ghidra.test.AbstractGhidraHeadedIntegrationTest;
 import ghidra.util.task.TaskMonitor;
 
-public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest {
+public class DefaultProjectDataTest extends AbstractGhidraHeadedIntegrationTest {
 
 	private File privateProjectDir;
 	private File sharedProjectDir;
 	private FileSystem sharedFS;
 	private LocalFileSystem privateFS;
-	private ProjectFileManager fileMgr;
+	private DefaultProjectData projectData;
 	private DomainFolder root;
 	private List<MyEvent> events = new ArrayList<>();
 
@@ -83,9 +84,9 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 		sharedFS = LocalFileSystem.getLocalFileSystem(sharedProjectDir.getAbsolutePath(), false,
 			true, false, true);
 
-		fileMgr = new ProjectFileManager(privateFS, sharedFS);
-		fileMgr.addDomainFolderChangeListener(new MyDomainFolderChangeListener());
-		root = fileMgr.getRootFolder();
+		projectData = new DefaultProjectData(privateFS, sharedFS);
+		projectData.addDomainFolderChangeListener(new MyDomainFolderChangeListener());
+		root = projectData.getRootFolder();
 		flushFileSystemEventsAndClearTestQueue();
 	}
 
@@ -97,7 +98,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 	@After
 	public void tearDown() {
-		fileMgr.dispose();
+		projectData.dispose();
 		deleteAll(privateProjectDir);
 		deleteAll(sharedProjectDir);
 	}
@@ -136,9 +137,15 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 		}
 	}
 
+	@Test
+	public void testGetLocalProjectURL() {
+		assertEquals(GhidraURL.makeURL(projectData.getProjectLocator()),
+			projectData.getLocalProjectURL());
+	}
+
 	@Test
 	public void testGetRootFolder() throws Exception {
-		DomainFolder rootFolder = fileMgr.getRootFolder();
+		DomainFolder rootFolder = projectData.getRootFolder();
 		assertEquals("/", rootFolder.getPathname());
 		assertEquals(3, rootFolder.getFolders().length);
 	}
@@ -146,11 +153,11 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 	@Test
 	public void testGetFolder() throws Exception {
 
-		DomainFolder rootFolder = fileMgr.getRootFolder();
-		DomainFolder df1 = fileMgr.getFolder("/");
-		DomainFolder df2 = fileMgr.getFolder("/a");
-		DomainFolder df3 = fileMgr.getFolder("/a/y");
-		DomainFolder df4 = fileMgr.getFolder("/a/x");
+		DomainFolder rootFolder = projectData.getRootFolder();
+		DomainFolder df1 = projectData.getFolder("/");
+		DomainFolder df2 = projectData.getFolder("/a");
+		DomainFolder df3 = projectData.getFolder("/a/y");
+		DomainFolder df4 = projectData.getFolder("/a/x");
 
 		assertNotNull(rootFolder);
 		assertEquals(rootFolder, df1);
@@ -178,7 +185,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 	@Test
 	public void testCreateFile() throws Exception {
-		DomainFolder folder = fileMgr.getFolder("/a");
+		DomainFolder folder = projectData.getFolder("/a");
 		folder.getFiles(); // visit folder to receive change events from this folder
 		flushFileSystemEventsAndClearTestQueue();
 
@@ -195,18 +202,18 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 		assertEventsSize(2);
 		checkEvent(events.get(1), "File Added", null, null, "/a/file2", null, null);
 
-		DomainFile df = fileMgr.getFileByID(fileID1);
+		DomainFile df = projectData.getFileByID(fileID1);
 		assertNotNull(df);
 		assertEquals("file1", df.getName());
 		assertTrue(!df.isVersioned());
 
-		df = fileMgr.getFileByID(fileID2);
+		df = projectData.getFileByID(fileID2);
 		assertNotNull(df2);
 		assertEquals("file2", df.getName());
 
 		df1.addToVersionControl("", false, TaskMonitor.DUMMY);
 
-		df = fileMgr.getFileByID(fileID1);
+		df = projectData.getFileByID(fileID1);
 		assertNotNull(df1);
 		assertEquals("file1", df.getName());
 		assertTrue(df.isVersioned());
@@ -216,7 +223,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 	@Test
 	public void testFileIndex() throws Exception {
 
-		DomainFileIndex fileIndex = (DomainFileIndex) getInstanceField("fileIndex", fileMgr);
+		DomainFileIndex fileIndex = (DomainFileIndex) getInstanceField("fileIndex", projectData);
 		assertNotNull(fileIndex);
 
 		@SuppressWarnings("unchecked")
@@ -224,21 +231,21 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 			(HashMap<String, String>) getInstanceField("fileIdToPathIndex", fileIndex);
 		assertNotNull(fileIdToPathIndex);
 
-		DomainFolder folder = fileMgr.getFolder("/a");
+		DomainFolder folder = projectData.getFolder("/a");
 
 		DomainFile df1 = createFile(folder, "file1");
 		String fileID = df1.getFileID();
 
-		assertEquals(df1, fileMgr.getFileByID(fileID));
+		assertEquals(df1, projectData.getFileByID(fileID));
 
 		// invalidate folder data to force search
 
-		GhidraFolderData rootFolderData = fileMgr.getRootFolderData();
+		GhidraFolderData rootFolderData = projectData.getRootFolderData();
 		rootFolderData.dispose();
 
 		assertTrue(fileIdToPathIndex.isEmpty()); // folder invalidation should cause map to clear
 
-		assertEquals(df1, fileMgr.getFileByID(fileID));
+		assertEquals(df1, projectData.getFileByID(fileID));
 
 		assertFalse(fileIdToPathIndex.isEmpty()); // index should become populated
 	}
@@ -246,7 +253,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 	@Test
 	public void testFileIndexUndoCheckout() throws Exception {
 // TODO: This only tests the connected state - a remote file-system is required to test the disconnect/re-connected condition
-		DomainFolder folder = fileMgr.getFolder("/a");
+		DomainFolder folder = projectData.getFolder("/a");
 
 		DomainFile df1 = createFile(folder, "file1");
 		String fileID = df1.getFileID();
@@ -265,7 +272,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 	@Test
 	public void testFileIndexHijack() throws Exception {
 // TODO: This only tests the connected state - a remote file-system is required to test the disconnect/re-connected condition
-		DomainFolder folder = fileMgr.getFolder("/a");
+		DomainFolder folder = projectData.getFolder("/a");
 		folder.getFiles(); // visit folder to enable folder change listener
 
 		// create shared file /a/file1 and keep checked-out
@@ -285,7 +292,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 		df1.setName("file2");
 
-		DomainFile df2 = fileMgr.getFile("/a/file2");
+		DomainFile df2 = projectData.getFile("/a/file2");
 
 		assertTrue(!fileID.equals(df2.getFileID()));
 
@@ -451,7 +458,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 	@Test
 	public void testFolderRenamedEvent3() throws Exception {
-		fileMgr.getFolder("/a"); // force folder refresh to reduce event count
+		projectData.getFolder("/a"); // force folder refresh to reduce event count
 		flushFileSystemEventsAndClearTestQueue();
 
 		// exists in localFS so "b" folder should not get created again
@@ -495,7 +502,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 	@Test
 	public void testRenameFolder6() throws Exception {
-		DomainFolder aFolder = fileMgr.getFolder("/a");
+		DomainFolder aFolder = projectData.getFolder("/a");
 		assertNotNull(aFolder);
 		aFolder.getFolders(); // visit folder to receive change events for it
 
@@ -601,12 +608,12 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 
 		// versioned folder was moved to /c/a, but private folder /a should still exist
 
-		GhidraFolder folder = (GhidraFolder) fileMgr.getFolder("/a");
+		GhidraFolder folder = (GhidraFolder) projectData.getFolder("/a");
 		assertNotNull(folder);
 		assertTrue(folder.privateExists());
 		assertFalse(folder.sharedExists());
 
-		folder = (GhidraFolder) fileMgr.getFolder("/c/a");
+		folder = (GhidraFolder) projectData.getFolder("/c/a");
 		assertNotNull(folder);
 		assertFalse(folder.privateExists());
 		assertTrue(folder.sharedExists());

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/data/GhidraFileTest.java

@@ -41,7 +41,7 @@ public class GhidraFileTest extends AbstractGhidraHeadedIntegrationTest {
 	private FileSystem sharedFS;
 	private LocalFileSystem privateFS;
 
-	private ProjectFileManager pfm;
+	private DefaultProjectData projectData;
 	private GhidraFolder root;
 
 	public GhidraFileTest() {
@@ -76,8 +76,8 @@ public class GhidraFileTest extends AbstractGhidraHeadedIntegrationTest {
 			false, false, true);
 		sharedFS = LocalFileSystem.getLocalFileSystem(sharedProjectDir.getAbsolutePath(), false,
 			true, false, true);
-		pfm = new ProjectFileManager(privateFS, sharedFS);
-		root = pfm.getRootFolder();
+		projectData = new DefaultProjectData(privateFS, sharedFS);
+		root = projectData.getRootFolder();
 
 	}
 
@@ -88,12 +88,12 @@ public class GhidraFileTest extends AbstractGhidraHeadedIntegrationTest {
 	}
 
 	@Test
-	public void testLocalURL() throws IOException {
+	public void testGetLocalProjectURL() throws IOException {
 		createDB(privateFS, "/a", "file1");
-		assertEquals(GhidraURL.makeURL(pfm.getProjectLocator(), "/a/file1", "xyz"),
-			pfm.getFile("/a/file1").getLocalProjectURL("xyz"));
-		assertEquals(GhidraURL.makeURL(pfm.getProjectLocator(), "/a/file1", null),
-			pfm.getFile("/a/file1").getLocalProjectURL(null));
+		assertEquals(GhidraURL.makeURL(projectData.getProjectLocator(), "/a/file1", "xyz"),
+			projectData.getFile("/a/file1").getLocalProjectURL("xyz"));
+		assertEquals(GhidraURL.makeURL(projectData.getProjectLocator(), "/a/file1", null),
+			projectData.getFile("/a/file1").getLocalProjectURL(null));
 	}
 
 	@Test
@@ -345,7 +345,7 @@ public class GhidraFileTest extends AbstractGhidraHeadedIntegrationTest {
 
 	private void refresh() throws IOException {
 		// refresh everything regardless of visited state
-		pfm.refresh(true);
+		projectData.refresh(true);
 	}
 
 	private void deleteAll(File file) {

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/data/GhidraFolderTest.java

@@ -22,6 +22,8 @@ import java.io.IOException;
 
 import org.junit.*;
 
+import ghidra.framework.model.ProjectLocator;
+import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.store.local.LocalFileSystem;
 import ghidra.test.AbstractGhidraHeadedIntegrationTest;
 
@@ -31,6 +33,7 @@ public class GhidraFolderTest extends AbstractGhidraHeadedIntegrationTest {
 	private LocalFileSystem sharedFS;
 	private LocalFileSystem privateFS;
 
+	private DefaultProjectData projectData;
 	private GhidraFolder root;
 
 	public GhidraFolderTest() {
@@ -68,8 +71,8 @@ public class GhidraFolderTest extends AbstractGhidraHeadedIntegrationTest {
 			false, false, true);
 		sharedFS = LocalFileSystem.getLocalFileSystem(sharedProjectDir.getAbsolutePath(), false,
 			true, false, true);
-		ProjectFileManager projectFileManager = new ProjectFileManager(privateFS, sharedFS);
-		root = projectFileManager.getRootFolder();
+		projectData = new DefaultProjectData(privateFS, sharedFS);
+		root = projectData.getRootFolder();
 	}
 
 	private void deleteTestFiles() {
@@ -82,6 +85,15 @@ public class GhidraFolderTest extends AbstractGhidraHeadedIntegrationTest {
 		deleteTestFiles();
 	}
 
+	@Test
+	public void testGetLocalProjectURL() {
+		ProjectLocator projectLocator = projectData.getProjectLocator();
+		assertEquals(GhidraURL.makeURL(projectLocator, "/a/y", null),
+			projectData.getFolder("/a/y").getLocalProjectURL());
+		assertEquals(GhidraURL.makeURL(projectLocator, "/a/x", null),
+			projectData.getFolder("/a/x").getLocalProjectURL());
+	}
+
 	@Test
 	public void testGetFolderNames() throws Exception {
 		GhidraFolder[] folders = root.getFolders();

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/data/IndexedFileSystemFolderTest.java

@@ -15,24 +15,23 @@
  */
 package ghidra.framework.data;
 
-import ghidra.framework.model.DomainFolder;
-import ghidra.framework.model.Project;
-import ghidra.framework.store.local.LocalFileSystem;
-import ghidra.test.AbstractGhidraHeadedIntegrationTest;
-import ghidra.util.InvalidNameException;
-
 import java.io.File;
 import java.io.IOException;
 
 import org.junit.*;
 
+import ghidra.framework.model.DomainFolder;
+import ghidra.framework.store.local.LocalFileSystem;
+import ghidra.test.AbstractGhidraHeadedIntegrationTest;
+import ghidra.util.InvalidNameException;
+
 public class IndexedFileSystemFolderTest extends AbstractGhidraHeadedIntegrationTest {
 
 	private File testRootDir;
 	private File privateProjectDir;
 	private File sharedProjectDir;
 	private DomainFolder root;
-	private Project project;
+
 	private LocalFileSystem sharedFS;
 	private LocalFileSystem privateFS;
 
@@ -52,8 +51,8 @@ public class IndexedFileSystemFolderTest extends AbstractGhidraHeadedIntegration
 			true, false, false);
 		sharedFS = LocalFileSystem.getLocalFileSystem(sharedProjectDir.getAbsolutePath(), true,
 			true, false, false);
-		ProjectFileManager projectFileManager = new ProjectFileManager(privateFS, sharedFS);
-		root = projectFileManager.getRootFolder();
+		DefaultProjectData projectData = new DefaultProjectData(privateFS, sharedFS);
+		root = projectData.getRootFolder();
 	}
 
 	@After
@@ -68,8 +67,8 @@ public class IndexedFileSystemFolderTest extends AbstractGhidraHeadedIntegration
 	private void deleteAll(File file) {
 		if (file.isDirectory()) {
 			File[] files = file.listFiles();
-			for (int i = 0; i < files.length; i++) {
-				deleteAll(files[i]);
+			for (File file2 : files) {
+				deleteAll(file2);
 			}
 		}
 		file.delete();

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/main/datatree/FrontEndPluginActionsTest.java

@@ -903,8 +903,8 @@ public class FrontEndPluginActionsTest extends AbstractGhidraHeadedIntegrationTe
 		//
 
 		//@formatter:off
-		Object projectFileManager = getInstanceField("fileManager", df);
-		invokeInstanceMethod("setDomainObject", projectFileManager,
+		Object projectData = getInstanceField("projectData", df);
+		invokeInstanceMethod("setDomainObject", projectData,
 			new Class[] { String.class, 	DomainObjectAdapter.class },
 			new Object[] { path, program }
 				);
@@ -962,8 +962,7 @@ public class FrontEndPluginActionsTest extends AbstractGhidraHeadedIntegrationTe
 			}
 		}
 
-		return new FrontEndProjectTreeContext(null, null, paths, folderList, fileList, tree,
-			true);
+		return new FrontEndProjectTreeContext(null, null, paths, folderList, fileList, tree, true);
 	}
 
 }

Ghidra/Features/Base/src/test.slow/java/ghidra/framework/project/AddViewToProjectTest.java

@@ -15,16 +15,18 @@
  */
 package ghidra.framework.project;
 
+import static org.junit.Assert.*;
+
 import java.net.URL;
 
 import org.junit.*;
 
-import generic.test.AbstractGenericTest;
-import ghidra.framework.model.Project;
-import ghidra.framework.model.ProjectLocator;
+import ghidra.framework.data.DefaultProjectData;
+import ghidra.framework.model.*;
 import ghidra.framework.protocol.ghidra.GhidraURL;
-import ghidra.test.AbstractGhidraHeadlessIntegrationTest;
-import ghidra.test.ProjectTestUtils;
+import ghidra.test.*;
+import ghidra.util.Msg;
+import ghidra.util.task.TaskMonitor;
 
 /**
  * Test class for adding and a view to a project, and removing
@@ -32,7 +34,7 @@ import ghidra.test.ProjectTestUtils;
  */
 public class AddViewToProjectTest extends AbstractGhidraHeadlessIntegrationTest {
 
-	private final static String DIRECTORY_NAME = AbstractGenericTest.getTestDirectoryPath();
+	private final static String DIRECTORY_NAME = getTestDirectoryPath();
 	private final static String PROJECT_NAME1 = "TestAddViewToProject";
 	private final static String PROJECT_VIEW1 = "TestView1";
 	private final static String PROJECT_VIEW2 = "TestView2";
@@ -52,24 +54,9 @@ public class AddViewToProjectTest extends AbstractGhidraHeadlessIntegrationTest
 		ProjectTestUtils.deleteProject(DIRECTORY_NAME, PROJECT_VIEW2);
 	}
 
-	/**
-	 * Do the test.
-	 * @param args same args that are passed to RegressionTester.main()
-	 */
 	@Test
 	public void testAddToView() throws Exception {
 
-//        String filename =  System.getProperty("user.dir") +
-//            File.separator + "testGhidraPreferences";
-//
-//        try {
-//            Preferences.load(filename);
-//
-//        } catch (IOException e) {
-//        }
-//
-//        Preferences.setFilename(filename);
-
 		// make sure we have projects to use as the project view...
 		ProjectTestUtils.getProject(DIRECTORY_NAME, PROJECT_VIEW1).close();
 		ProjectTestUtils.getProject(DIRECTORY_NAME, PROJECT_VIEW2).close();
@@ -87,12 +74,12 @@ public class AddViewToProjectTest extends AbstractGhidraHeadlessIntegrationTest
 			// validate the view was added to project
 			ProjectLocator[] projViews = project.getProjectViews();
 			for (ProjectLocator projView : projViews) {
-				System.out.println("added view: " + projView);
+				Msg.debug(this, "** added view: " + projView);
 			}
 
 			// remove the view...
 			project.removeProjectView(view);
-			System.out.println("removed view: " + view);
+			Msg.debug(this, "** removed view: " + view);
 
 			projViews = project.getProjectViews();
 			for (ProjectLocator projView : projViews) {
@@ -106,4 +93,59 @@ public class AddViewToProjectTest extends AbstractGhidraHeadlessIntegrationTest
 		}
 	}
 
+	@Test
+	public void testCloseViewWithOpenProgram() throws Exception {
+
+		DomainObject dobj = null;
+
+		// make sure we have projects to use as the project view...
+		Project project = ProjectTestUtils.getProject(DIRECTORY_NAME, PROJECT_VIEW1);
+		try {
+			ToyProgramBuilder builder = new ToyProgramBuilder("Test", true);
+			DomainFolder rootFolder = project.getProjectData().getRootFolder();
+			rootFolder.createFile("Test", builder.getProgram(), TaskMonitor.DUMMY);
+			builder.dispose();
+			project.close();
+
+			// get project (create it if it doesn't exist...)
+			project = ProjectTestUtils.getProject(DIRECTORY_NAME, PROJECT_NAME1);
+
+			URL view = GhidraURL.makeURL(DIRECTORY_NAME, PROJECT_VIEW1);
+			DefaultProjectData projectData =
+				(DefaultProjectData) project.addProjectView(view, true);
+			Msg.debug(this, "** added view: " + view);
+			assertNotNull(projectData);
+
+			DomainFile f = projectData.getFile("/Test");
+			assertNotNull(f);
+
+			// Open file and hold onto
+			dobj = f.getDomainObject(this, true, false, TaskMonitor.DUMMY);
+			Msg.debug(this, "** opened program: " + f);
+
+			assertFalse(projectData.isClosed());
+			assertFalse(projectData.isDisposed());
+
+			// remove the view while program open...
+			project.removeProjectView(view);
+			Msg.debug(this, "** removed view: " + view);
+
+			assertTrue(projectData.isClosed());
+			assertFalse(projectData.isDisposed());
+
+			Msg.debug(this, "** releasing program: " + f);
+			dobj.release(this);
+			dobj = null;
+
+			assertTrue(projectData.isClosed());
+			assertTrue(projectData.isDisposed());
+		}
+		finally {
+			if (dobj != null) {
+				dobj.release(this);
+			}
+			project.close();
+		}
+	}
+
 }

Ghidra/Features/Base/src/test.slow/java/ghidra/program/database/ProgramUserDataTest.java

@@ -24,7 +24,7 @@ import java.util.Set;
 import org.junit.*;
 
 import generic.test.AbstractGTest;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.*;
 import ghidra.program.model.address.Address;
 import ghidra.program.model.address.AddressSpace;
@@ -57,8 +57,8 @@ public class ProgramUserDataTest extends AbstractGhidraHeadedIntegrationTest {
 		projectLocator = new ProjectLocator(TEMP, "Test");
 		project = TestProjectManager.get().createProject(projectLocator, null, true);
 		dataDir =
-			new File(projectLocator.getProjectDir(), ProjectFileManager.INDEXED_DATA_FOLDER_NAME);
-		userDir = new File(projectLocator.getProjectDir(), ProjectFileManager.USER_FOLDER_NAME);
+			new File(projectLocator.getProjectDir(), DefaultProjectData.INDEXED_DATA_FOLDER_NAME);
+		userDir = new File(projectLocator.getProjectDir(), DefaultProjectData.USER_FOLDER_NAME);
 
 		ProgramBuilder builder = new ProgramBuilder("Test", ProgramBuilder._TOY);
 		df = project.getProjectData()

Ghidra/Features/Base/src/test/java/ghidra/base/project/FakeSharedProject.java

@@ -81,8 +81,8 @@ public class FakeSharedProject {
 	// Note: this how we share multiple projects
 	void setVersionedFileSystem(LocalFileSystem fs) {
 
-		ProjectFileManager fm = getProjectFileManager();
-		invokeInstanceMethod("setVersionedFileSystem", fm, argTypes(FileSystem.class), args(fs));
+		DefaultProjectData pd = getProjectData();
+		invokeInstanceMethod("setVersionedFileSystem", pd, argTypes(FileSystem.class), args(fs));
 	}
 
 	/**
@@ -94,12 +94,12 @@ public class FakeSharedProject {
 	}
 
 	/**
-	 * Gets the project file manager
+	 * Gets the project data instance
 	 * 
-	 * @return the project file manager
+	 * @return the project data instance
 	 */
-	public ProjectFileManager getProjectFileManager() {
-		return (ProjectFileManager) gProject.getProjectData();
+	public DefaultProjectData getProjectData() {
+		return (DefaultProjectData) gProject.getProjectData();
 	}
 
 	/**
@@ -108,8 +108,8 @@ public class FakeSharedProject {
 	 * @return the root folder of this project
 	 */
 	public RootGhidraFolder getRootFolder() {
-		ProjectFileManager pfm = getProjectFileManager();
-		return (RootGhidraFolder) pfm.getRootFolder();
+		DefaultProjectData pd = getProjectData();
+		return (RootGhidraFolder) pd.getRootFolder();
 	}
 
 	/**
@@ -181,6 +181,7 @@ public class FakeSharedProject {
 	 * 	<li>calling {@link #addDomainFile(String)}</li>
 	 *  <li>Adding a versioned file to another project that shares the same repo with this project</li>
 	 * </ul>
+	 * @param parentPath the parent folder path
 	 * @param filename the filename
 	 * @return the file
 	 */
@@ -194,8 +195,7 @@ public class FakeSharedProject {
 	 * Creates a folder by the given name in the given parent folder, creating the parent 
 	 * folder if needed
 	 * 
-	 * @param parentPath the parent folder path
-	 * @param name the name of the folder to create
+	 * @param path the full path of the folder to create
 	 * @return the created folder
 	 * @throws Exception if there are any exceptions creating the folder
 	 */
@@ -367,7 +367,7 @@ public class FakeSharedProject {
 	 * @see FakeRepository#dispose()
 	 */
 	public void dispose() {
-		ProjectLocator projectLocator = getProjectFileManager().getProjectLocator();
+		ProjectLocator projectLocator = getProjectData().getProjectLocator();
 		programManager.disposeOpenPrograms();
 		gProject.close();
 		FileUtilities.deleteDir(projectLocator.getProjectDir());
@@ -388,7 +388,7 @@ public class FakeSharedProject {
 		}
 
 		ProjectLocator pl = df.getProjectLocator();
-		ProjectLocator mypl = getProjectFileManager().getProjectLocator();
+		ProjectLocator mypl = getProjectData().getProjectLocator();
 		if (!pl.equals(mypl)) {
 			throw new IllegalArgumentException("Domain file '" + df + "' is not in this project: " +
 				mypl.getName() + "\nYou must call addDomainFile(filename).");
@@ -397,9 +397,8 @@ public class FakeSharedProject {
 
 	private void waitForFileSystemEvents() {
 		LocalFileSystem versionedFileSystem = getVersionedFileSystem();
-		FileSystemEventManager eventManager =
-			(FileSystemEventManager) TestUtils.getInstanceField("eventManager",
-				versionedFileSystem);
+		FileSystemEventManager eventManager = (FileSystemEventManager) TestUtils
+				.getInstanceField("eventManager", versionedFileSystem);
 
 		eventManager.flushEvents(DEFAULT_WAIT_TIMEOUT, TimeUnit.MILLISECONDS);
 	}
@@ -444,16 +443,16 @@ public class FakeSharedProject {
 	}
 
 	LocalFileSystem getVersionedFileSystem() {
-		ProjectFileManager fileManager = getProjectFileManager();
+		DefaultProjectData projectData = getProjectData();
 		LocalFileSystem fs =
-			(LocalFileSystem) TestUtils.invokeInstanceMethod("getVersionedFileSystem", fileManager);
+			(LocalFileSystem) TestUtils.invokeInstanceMethod("getVersionedFileSystem", projectData);
 		return fs;
 	}
 
 	void refresh() {
-		ProjectFileManager fileManager = getProjectFileManager();
+		DefaultProjectData projectData = getProjectData();
 		try {
-			fileManager.refresh(true);
+			projectData.refresh(true);
 		}
 		catch (IOException e) {
 			// shouldn't happen

Ghidra/Features/FileFormats/ghidra_scripts/MergeTwoProgramsScript.java

@@ -33,215 +33,219 @@ import ghidra.program.model.listing.*;
 import ghidra.program.model.mem.*;
 import ghidra.program.model.symbol.*;
 
-
 public class MergeTwoProgramsScript extends GhidraScript {
 
 	@Override
 	protected void run() throws Exception {
 
-		if ( currentProgram == null ) {
-			printerr( "Please open a program first!" );
+		if (currentProgram == null) {
+			printerr("Please open a program first!");
 			return;
 		}
 
-		Program otherProgram = askProgram( "Select program from which to merge: " );
+		Program otherProgram = askProgram("Select program from which to merge: ");
 
-		if ( otherProgram == null ) {
-			printerr( "Please select the other program first!" );
+		if (otherProgram == null) {
+			printerr("Please select the other program first!");
 			return;
 		}
 
-		if ( !currentProgram.getLanguage().equals( otherProgram.getLanguage() ) ) {
-			printerr( "Incompatible program languages!" );
+		try {
+
+			if (!currentProgram.getLanguage().equals(otherProgram.getLanguage())) {
+				printerr("Incompatible program languages!");
 				return;
 			}
 
-		if ( currentProgram.getMemory().intersects( otherProgram.getMemory() ) ) {
-			printerr( "Memory map of current program must be disjoint from other program!" );
+			if (currentProgram.getMemory().intersects(otherProgram.getMemory())) {
+				printerr("Memory map of current program must be disjoint from other program!");
 				return;
 			}
 
-		openProgram( currentProgram );
+			openProgram(currentProgram);
 
-		mergeMemory      ( currentProgram, otherProgram );
-		mergeSymbols     ( currentProgram, otherProgram );
-		mergeBookmarks   ( currentProgram, otherProgram );
-		mergeComments    ( currentProgram, otherProgram );
-		mergeData        ( currentProgram, otherProgram );
-		mergeInstructions( currentProgram, otherProgram );
-		mergeEquates     ( currentProgram, otherProgram );
-		mergeReferences  ( currentProgram, otherProgram );
+			mergeMemory(currentProgram, otherProgram);
+			mergeSymbols(currentProgram, otherProgram);
+			mergeBookmarks(currentProgram, otherProgram);
+			mergeComments(currentProgram, otherProgram);
+			mergeData(currentProgram, otherProgram);
+			mergeInstructions(currentProgram, otherProgram);
+			mergeEquates(currentProgram, otherProgram);
+			mergeReferences(currentProgram, otherProgram);
+		}
+		finally {
+			otherProgram.release(this);
+		}
 	}
 
-	private void mergeReferences( Program currProgram, Program otherProgram ) {
-		monitor.setMessage( "Merging references..." );
+	private void mergeReferences(Program currProgram, Program otherProgram) {
+		monitor.setMessage("Merging references...");
 		ReferenceManager currentReferenceManager = currProgram.getReferenceManager();
 		ReferenceManager otherReferenceManager = otherProgram.getReferenceManager();
-		ReferenceIterator otherReferenceIterator = otherReferenceManager.getReferenceIterator( otherProgram.getMinAddress() );
-		while ( otherReferenceIterator.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		ReferenceIterator otherReferenceIterator =
+			otherReferenceManager.getReferenceIterator(otherProgram.getMinAddress());
+		while (otherReferenceIterator.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Reference otherReference = otherReferenceIterator.next();
-			if ( otherReference.isStackReference() ) {
+			if (otherReference.isStackReference()) {
 				continue;
 			}
-			currentReferenceManager.addReference( otherReference );
+			currentReferenceManager.addReference(otherReference);
 		}
 	}
 
-	private void mergeInstructions( Program currProgram, Program otherProgram ) {
-		monitor.setMessage( "Merging instructions..." );
+	private void mergeInstructions(Program currProgram, Program otherProgram) {
+		monitor.setMessage("Merging instructions...");
 		Listing currentListing = currProgram.getListing();
 		Listing otherListing = otherProgram.getListing();
-		InstructionIterator otherInstructions = otherListing.getInstructions( true );
-		while ( otherInstructions.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		InstructionIterator otherInstructions = otherListing.getInstructions(true);
+		while (otherInstructions.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Instruction otherInstruction = otherInstructions.next();
-			if ( currentListing.isUndefined( otherInstruction.getMinAddress(), otherInstruction.getMaxAddress() ) ) {
-				disassemble( otherInstruction.getMinAddress() );
+			if (currentListing.isUndefined(otherInstruction.getMinAddress(),
+				otherInstruction.getMaxAddress())) {
+				disassemble(otherInstruction.getMinAddress());
 			}
 		}
 	}
 
-	private void mergeEquates( Program currProgram, Program otherProgram ) throws Exception {
-		monitor.setMessage( "Merging equates..." );
+	private void mergeEquates(Program currProgram, Program otherProgram) throws Exception {
+		monitor.setMessage("Merging equates...");
 		EquateTable currentEquateTable = currProgram.getEquateTable();
 		EquateTable otherEquateTable = otherProgram.getEquateTable();
 		Iterator<Equate> otherEquates = otherEquateTable.getEquates();
-		while ( otherEquates.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		while (otherEquates.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Equate otherEquate = otherEquates.next();
-			Equate currentEquate = currentEquateTable.createEquate( otherEquate.getName(), otherEquate.getValue() );
-			EquateReference [] otherEquateReferences = otherEquate.getReferences();
-			for ( EquateReference otherEquateReference : otherEquateReferences ) {
-				if ( monitor.isCancelled() ) {
+			Equate currentEquate =
+				currentEquateTable.createEquate(otherEquate.getName(), otherEquate.getValue());
+			EquateReference[] otherEquateReferences = otherEquate.getReferences();
+			for (EquateReference otherEquateReference : otherEquateReferences) {
+				if (monitor.isCancelled()) {
 					break;
 				}
-				currentEquate.addReference( otherEquateReference.getAddress(), otherEquateReference.getOpIndex() );
+				currentEquate.addReference(otherEquateReference.getAddress(),
+					otherEquateReference.getOpIndex());
 			}
 		}
 	}
 
-	private void mergeData( Program currProgram, Program otherProgram ) throws Exception {
-		monitor.setMessage( "Merging data..." );
+	private void mergeData(Program currProgram, Program otherProgram) throws Exception {
+		monitor.setMessage("Merging data...");
 		Listing currentListing = currProgram.getListing();
 		Listing otherListing = otherProgram.getListing();
-		DataIterator otherDataIterator = otherListing.getDefinedData( true );
-		while ( otherDataIterator.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		DataIterator otherDataIterator = otherListing.getDefinedData(true);
+		while (otherDataIterator.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Data otherData = otherDataIterator.next();
-			if ( currentListing.isUndefined( otherData.getMinAddress(), otherData.getMaxAddress() ) ) {
-				currentListing.createData( otherData.getMinAddress(), otherData.getDataType() );
+			if (currentListing.isUndefined(otherData.getMinAddress(), otherData.getMaxAddress())) {
+				currentListing.createData(otherData.getMinAddress(), otherData.getDataType());
 			}
 		}
 	}
 
-	private void mergeComments( Program currProgram, Program otherProgram ) throws Exception {
-		monitor.setMessage( "Merging comments..." );
-		int [] commentTypes = {
-			CodeUnit.EOL_COMMENT,
-			CodeUnit.PRE_COMMENT,
-			CodeUnit.POST_COMMENT,
-			CodeUnit.PLATE_COMMENT,
-			CodeUnit.REPEATABLE_COMMENT,
-		};
+	private void mergeComments(Program currProgram, Program otherProgram) throws Exception {
+		monitor.setMessage("Merging comments...");
+		int[] commentTypes = { CodeUnit.EOL_COMMENT, CodeUnit.PRE_COMMENT, CodeUnit.POST_COMMENT,
+			CodeUnit.PLATE_COMMENT, CodeUnit.REPEATABLE_COMMENT, };
 		Listing currentListing = currProgram.getListing();
 		Listing otherListing = otherProgram.getListing();
-		CodeUnitIterator otherCodeUnits = otherListing.getCodeUnits( true );
-		while ( otherCodeUnits.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		CodeUnitIterator otherCodeUnits = otherListing.getCodeUnits(true);
+		while (otherCodeUnits.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			CodeUnit otherCodeUnit = otherCodeUnits.next();
-			for ( int commentType : commentTypes ) {
-				if ( monitor.isCancelled() ) {
+			for (int commentType : commentTypes) {
+				if (monitor.isCancelled()) {
 					break;
 				}
-				String otherComment = otherCodeUnit.getComment( commentType );
-				if ( otherComment != null ) {
-					currentListing.setComment( otherCodeUnit.getAddress(), commentType, otherComment );
+				String otherComment = otherCodeUnit.getComment(commentType);
+				if (otherComment != null) {
+					currentListing.setComment(otherCodeUnit.getAddress(), commentType,
+						otherComment);
 				}
 			}
 		}
 	}
 
-	private void mergeBookmarks( Program currProgram, Program otherProgram ) {
-		monitor.setMessage( "Merging bookmarks..." );
+	private void mergeBookmarks(Program currProgram, Program otherProgram) {
+		monitor.setMessage("Merging bookmarks...");
 		BookmarkManager currentBookmarkManager = currProgram.getBookmarkManager();
 		BookmarkManager otherBookmarkManager = otherProgram.getBookmarkManager();
 		Iterator<Bookmark> otherBookmarks = otherBookmarkManager.getBookmarksIterator();
-		while ( otherBookmarks.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		while (otherBookmarks.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Bookmark otherBookmark = otherBookmarks.next();
-			currentBookmarkManager.setBookmark( otherBookmark.getAddress(),
-				otherBookmark.getTypeString(),
-				otherBookmark.getCategory(),
-				otherBookmark.getComment() );
+			currentBookmarkManager.setBookmark(otherBookmark.getAddress(),
+				otherBookmark.getTypeString(), otherBookmark.getCategory(),
+				otherBookmark.getComment());
 		}
 	}
 
-	private void mergeSymbols( Program currProgram, Program otherProgram ) throws Exception {
-		monitor.setMessage( "Merging symbols..." );
+	private void mergeSymbols(Program currProgram, Program otherProgram) throws Exception {
+		monitor.setMessage("Merging symbols...");
 		SymbolTable currentSymbolTable = currProgram.getSymbolTable();
 		SymbolTable otherSymbolTable = otherProgram.getSymbolTable();
-		SymbolIterator otherSymbols = otherSymbolTable.getAllSymbols( false );
-		while ( otherSymbols.hasNext() ) {
-			if ( monitor.isCancelled() ) {
+		SymbolIterator otherSymbols = otherSymbolTable.getAllSymbols(false);
+		while (otherSymbols.hasNext()) {
+			if (monitor.isCancelled()) {
 				break;
 			}
 			Symbol otherSymbol = otherSymbols.next();
-			if ( otherSymbol.isDynamic() ) {
+			if (otherSymbol.isDynamic()) {
 				continue;
 			}
 			try {
 				Namespace otherNamespace = otherSymbol.getParentNamespace();
-				Namespace currentNamespace = mirrorNamespace( currProgram, otherProgram, otherNamespace );
-				if ( otherSymbol.getSymbolType() == SymbolType.FUNCTION ) {
-					Function otherFunction = otherProgram.getListing().getFunctionAt( otherSymbol.getAddress() );
-					currProgram.getListing().createFunction( otherSymbol.getName(),
-						currentNamespace,
-						otherFunction.getEntryPoint(),
-						otherFunction.getBody(),
-						SourceType.USER_DEFINED );
+				Namespace currentNamespace =
+					mirrorNamespace(currProgram, otherProgram, otherNamespace);
+				if (otherSymbol.getSymbolType() == SymbolType.FUNCTION) {
+					Function otherFunction =
+						otherProgram.getListing().getFunctionAt(otherSymbol.getAddress());
+					currProgram.getListing()
+							.createFunction(otherSymbol.getName(), currentNamespace,
+								otherFunction.getEntryPoint(), otherFunction.getBody(),
+								SourceType.USER_DEFINED);
 				}
 				else {
-					currentSymbolTable.createLabel( otherSymbol.getAddress(),
-						otherSymbol.getName(),
-						currentNamespace,
-						SourceType.USER_DEFINED );
+					currentSymbolTable.createLabel(otherSymbol.getAddress(), otherSymbol.getName(),
+						currentNamespace, SourceType.USER_DEFINED);
 				}
 			}
-			catch ( Exception e ) {
-				printerr( "Unable to create symbol: " + otherSymbol.getName() );
+			catch (Exception e) {
+				printerr("Unable to create symbol: " + otherSymbol.getName());
 			}
 		}
 	}
 
-	private Namespace mirrorNamespace( Program currProgram, Program otherProgram, Namespace otherNamespace ) throws Exception {
-		if ( otherNamespace == null ) {
+	private Namespace mirrorNamespace(Program currProgram, Program otherProgram,
+			Namespace otherNamespace) throws Exception {
+		if (otherNamespace == null) {
 			return currProgram.getGlobalNamespace();
 		}
 		SourceType source = SourceType.USER_DEFINED;//this will be default, since we are running a script!
 		try {
 			source = otherNamespace.getSymbol().getSource();
 		}
-		catch ( Exception e ) {
+		catch (Exception e) {
 		}
 		return NamespaceUtils.createNamespaceHierarchy(otherNamespace.getName(true), null,
 			currProgram, source);
 	}
 
-	private void mergeMemory( Program currProgram, Program otherProgram ) throws Exception {
-		monitor.setMessage( "Merging memory..." );
+	private void mergeMemory(Program currProgram, Program otherProgram) throws Exception {
+		monitor.setMessage("Merging memory...");
 		Memory otherMemory = otherProgram.getMemory();
 		MemoryBlock[] otherBlocks = otherMemory.getBlocks();
 		MessageLog log = new MessageLog();

Ghidra/Features/VersionTracking/ghidra_scripts/AutoVersionTrackingScript.java

@@ -17,7 +17,6 @@
 // data and and then save the session.
 //@category Examples.Version Tracking
 
-import java.util.Iterator;
 import java.util.List;
 
 import ghidra.app.script.GhidraScript;
@@ -32,6 +31,21 @@ import ghidra.program.model.listing.Program;
 import ghidra.util.task.TaskLauncher;
 
 public class AutoVersionTrackingScript extends GhidraScript {
+
+	private Program sourceProgram;
+	private Program destinationProgram;
+
+	@Override
+	public void cleanup(boolean success) {
+		if (sourceProgram != null && sourceProgram.isUsedBy(this)) {
+			sourceProgram.release(this);
+		}
+		if (destinationProgram != null && destinationProgram.isUsedBy(this)) {
+			destinationProgram.release(this);
+		}
+		super.cleanup(success);
+	}
+
 	@Override
 	public void run() throws Exception {
 
@@ -39,9 +53,6 @@ public class AutoVersionTrackingScript extends GhidraScript {
 			askProjectFolder("Please choose a folder for your Version Tracking session.");
 		String name = askString("Please enter a Version Tracking session name", "Session Name");
 
-		Program sourceProgram;
-		Program destinationProgram;
-
 		boolean isCurrentProgramSourceProg = askYesNo("Current Program Source Program?",
 			"Is the current program your source program?");
 
@@ -54,6 +65,10 @@ public class AutoVersionTrackingScript extends GhidraScript {
 			sourceProgram = askProgram("Please select the source (existing annotated) program");
 		}
 
+		if (sourceProgram == null || destinationProgram == null) {
+			return;
+		}
+
 		// Need to end the script transaction or it interferes with vt things that need locks
 		end(true);
 
@@ -81,9 +96,7 @@ public class AutoVersionTrackingScript extends GhidraScript {
 
 	public static <T extends Plugin> T getPlugin(PluginTool tool, Class<T> c) {
 		List<Plugin> list = tool.getManagedPlugins();
-		Iterator<Plugin> it = list.iterator();
-		while (it.hasNext()) {
-			Plugin p = it.next();
+		for (Plugin p : list) {
 			if (p.getClass() == c) {
 				return c.cast(p);
 			}

Ghidra/Features/VersionTracking/ghidra_scripts/CreateAppliedExactMatchingSessionScript.java

@@ -17,6 +17,9 @@
 // data and and then save the session.
 //@category Examples.Version Tracking
 
+import java.util.Collection;
+import java.util.List;
+
 import ghidra.app.script.GhidraScript;
 import ghidra.feature.vt.api.correlator.program.*;
 import ghidra.feature.vt.api.db.VTSessionDB;
@@ -31,17 +34,35 @@ import ghidra.program.model.address.AddressSetView;
 import ghidra.program.model.listing.Program;
 import ghidra.util.exception.CancelledException;
 
-import java.util.Collection;
-import java.util.List;
-
 public class CreateAppliedExactMatchingSessionScript extends GhidraScript {
+
+	private Program sourceProgram;
+	private Program destinationProgram;
+
+	@Override
+	public void cleanup(boolean success) {
+		if (sourceProgram != null) {
+			sourceProgram.release(this);
+		}
+		if (destinationProgram != null) {
+			destinationProgram.release(this);
+		}
+		super.cleanup(success);
+	}
+
 	@Override
 	public void run() throws Exception {
 		DomainFolder folder =
 			askProjectFolder("Please choose a folder for the session domain object");
 		String name = askString("Please enter a Version Tracking session name", "Session Name");
-		Program sourceProgram = askProgram("Please select the source (existing annotated) program");
-		Program destinationProgram = askProgram("Please select the destination (new) program");
+		sourceProgram = askProgram("Please select the source (existing annotated) program");
+		if (sourceProgram == null) {
+			return;
+		}
+		destinationProgram = askProgram("Please select the destination (new) program");
+		if (destinationProgram == null) {
+			return;
+		}
 
 		VTSession session =
 			VTSessionDB.createVTSession(name, sourceProgram, destinationProgram, this);
@@ -58,7 +79,8 @@ public class CreateAppliedExactMatchingSessionScript extends GhidraScript {
 
 			// should we have convenience methods in VTCorrelator that don't
 			// take address sets, thus implying the entire address space should be used?
-			AddressSetView sourceAddressSet = sourceProgram.getMemory().getLoadedAndInitializedAddressSet();
+			AddressSetView sourceAddressSet =
+				sourceProgram.getMemory().getLoadedAndInitializedAddressSet();
 			AddressSetView destinationAddressSet =
 				destinationProgram.getMemory().getLoadedAndInitializedAddressSet();
 
@@ -91,17 +113,16 @@ public class CreateAppliedExactMatchingSessionScript extends GhidraScript {
 	private void correlateAndPossiblyApply(Program sourceProgram, Program destinationProgram,
 			VTSession session, PluginTool serviceProvider, VTAssociationManager manager,
 			AddressSetView sourceAddressSet, AddressSetView destinationAddressSet,
-			VTProgramCorrelatorFactory factory) throws CancelledException,
-			VTAssociationStatusException {
+			VTProgramCorrelatorFactory factory)
+			throws CancelledException, VTAssociationStatusException {
 
 		AddressSetView restrictedSourceAddresses =
 			excludeAcceptedMatches(session, sourceAddressSet, true);
 		AddressSetView restrictedDestinationAddresses =
 			excludeAcceptedMatches(session, destinationAddressSet, false);
 		VTOptions options = factory.createDefaultOptions();
-		VTProgramCorrelator correlator =
-			factory.createCorrelator(serviceProvider, sourceProgram, restrictedSourceAddresses,
-				destinationProgram, restrictedDestinationAddresses, options);
+		VTProgramCorrelator correlator = factory.createCorrelator(serviceProvider, sourceProgram,
+			restrictedSourceAddresses, destinationProgram, restrictedDestinationAddresses, options);
 
 		VTMatchSet results = correlator.correlate(session, monitor);
 		applyMatches(manager, results.getMatches());

Ghidra/Features/VersionTracking/ghidra_scripts/FindChangedFunctionsScript.java

@@ -29,6 +29,20 @@ import ghidra.util.Msg;
 
 public class FindChangedFunctionsScript extends GhidraVersionTrackingScript {
 
+	private Program p1;
+	private Program p2;
+
+	@Override
+	public void cleanup(boolean success) {
+		if (p1 != null) {
+			p1.release(this);
+		}
+		if (p2 != null) {
+			p2.release(this);
+		}
+		super.cleanup(success);
+	}
+
 	@Override
 	protected void run() throws Exception {
 		Project project = state.getProject();
@@ -39,13 +53,20 @@ public class FindChangedFunctionsScript extends GhidraVersionTrackingScript {
 		// Prompt the user to load the two programs that will be analyzed.
 		// This will only allow you to select programs from the currently-open 
 		// project in Ghidra, so import them if you haven't already.
-		Program p1 = askProgram("Program1_Version1");
-		Program p2 = askProgram("Program1_Version2");
+		p1 = askProgram("Program1_Version1");
+		if (p1 == null) {
+			return;
+		}
+		p2 = askProgram("Program1_Version2");
+		if (p2 == null) {
+			return;
+		}
 
 		// Make sure the selected programs are not open and locked by Ghidra. If so,
 		// warn the user.
 		if (areProgramsLocked(p1, p2)) {
-			Msg.showError(this, null, "Program is locked!", "One of the programs you selected is locked by Ghidra. Please correct and try again.");
+			Msg.showError(this, null, "Program is locked!",
+				"One of the programs you selected is locked by Ghidra. Please correct and try again.");
 			return;
 		}
 

Ghidra/Features/VersionTracking/src/main/java/ghidra/feature/vt/gui/actions/AutoVersionTrackingTask.java

@@ -82,7 +82,7 @@ public class AutoVersionTrackingTask extends Task {
 	private static int NUM_CORRELATORS = 8;
 
 	/**
-	 * Constructor for AutoVersionTrackingCommand
+	 * Constructor for a modal/blocking AutoVersionTrackingTask
 	 *
 	 * @param controller The Version Tracking controller for this session containing option and
 	 * tool information needed for this command.
@@ -483,8 +483,6 @@ public class AutoVersionTrackingTask extends Task {
 				continue;
 			}
 
-
-
 			// remove any matches that have identical source functions - if more than one
 			// with exactly the same instructions and operands then cannot determine a unique match
 			Set<Address> sourceAddresses = getSourceAddressesFromMatches(relatedMatches, monitor);

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DBWithUserDataContentHandler.java

@@ -73,7 +73,7 @@ public abstract class DBWithUserDataContentHandler<T extends DomainObjectAdapter
 			return;
 		}
 		String path = "/";
-		String name = ProjectFileManager.getUserDataFilename(associatedFileID);
+		String name = DefaultProjectData.getUserDataFilename(associatedFileID);
 		BufferFile bf = null;
 		boolean success = false;
 		try {
@@ -109,7 +109,7 @@ public abstract class DBWithUserDataContentHandler<T extends DomainObjectAdapter
 	public final void removeUserDataFile(FolderItem associatedItem, FileSystem userFilesystem)
 			throws IOException {
 		String path = "/";
-		String name = ProjectFileManager.getUserDataFilename(associatedItem.getFileID());
+		String name = DefaultProjectData.getUserDataFilename(associatedItem.getFileID());
 		FolderItem item = userFilesystem.getItem(path, name);
 		if (item != null) {
 			item.delete(-1, null);
@@ -130,7 +130,7 @@ public abstract class DBWithUserDataContentHandler<T extends DomainObjectAdapter
 			String associatedContentType, FileSystem userfs, TaskMonitor monitor)
 			throws IOException, CancelledException {
 		String path = "/";
-		String name = ProjectFileManager.getUserDataFilename(associatedFileID);
+		String name = DefaultProjectData.getUserDataFilename(associatedFileID);
 		FolderItem item = userfs.getItem(path, name);
 		if (item == null || !(item instanceof DatabaseItem) ||
 			!getUserDataContentType(associatedContentType).equals(item.getContentType())) {

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DefaultProjectData.java

@@ -16,12 +16,14 @@
 package ghidra.framework.data;
 
 import java.io.*;
+import java.net.URL;
 import java.util.*;
 
 import docking.widgets.OptionDialog;
 import generic.timer.GhidraSwinglessTimer;
 import ghidra.framework.client.*;
 import ghidra.framework.model.*;
+import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.remote.User;
 import ghidra.framework.store.*;
 import ghidra.framework.store.FileSystem;
@@ -37,9 +39,16 @@ import utilities.util.FileUtilities;
 /**
  * Helper class to manage files within a project.
  */
-public class ProjectFileManager implements ProjectData {
+public class DefaultProjectData implements ProjectData {
 
-	/**Name of folder that stores user's data*/
+	/**
+	 * {@code fileTrackingMap} is used to identify DefaultProjectData instances which are
+	 * tracking specific DomainObjectAdapter instances which are open.
+	 */
+	private static Map<DomainObjectAdapter, DefaultProjectData> fileTrackingMap =
+		Collections.synchronizedMap(new IdentityHashMap<>());
+
+	// Names of folders that stores project data
 	public static final String MANGLED_DATA_FOLDER_NAME = "data";
 	public static final String INDEXED_DATA_FOLDER_NAME = "idata";
 	public static final String USER_FOLDER_NAME = "user";
@@ -77,14 +86,17 @@ public class ProjectFileManager implements ProjectData {
 
 	private RootGhidraFolderData rootFolderData;
 
-	private Map<String, DomainObjectAdapter> openDomainObjects =
-		new HashMap<>();
+	private Map<String, DomainObjectAdapter> openDomainObjects = new HashMap<>();
 
 	private TaskMonitorAdapter projectDisposalMonitor = new TaskMonitorAdapter();
 
 	private ProjectLock projectLock;
 	private String owner;
 
+	private int inUseCount = 0; // open file count plus active merge sessions
+	private boolean closed = false;
+	private boolean disposed = false;
+
 	/**
 	 * Constructor for existing projects.
 	 * @param localStorageLocator the location of the project
@@ -96,7 +108,7 @@ public class ProjectFileManager implements ProjectData {
 	 * write lock (i.e., project in-use)
 	 * @throws FileNotFoundException if project directory not found
 	 */
-	public ProjectFileManager(ProjectLocator localStorageLocator, boolean isInWritableProject,
+	public DefaultProjectData(ProjectLocator localStorageLocator, boolean isInWritableProject,
 			boolean resetOwner) throws NotOwnerException, IOException, LockException {
 
 		this.localStorageLocator = localStorageLocator;
@@ -142,7 +154,7 @@ public class ProjectFileManager implements ProjectData {
 	 * @throws LockException if {@code isInWritableProject} is true and unable to establish project 
 	 * lock (i.e., project in-use)
 	 */
-	public ProjectFileManager(ProjectLocator localStorageLocator, RepositoryAdapter repository,
+	public DefaultProjectData(ProjectLocator localStorageLocator, RepositoryAdapter repository,
 			boolean isInWritableProject) throws IOException, LockException {
 		this.localStorageLocator = localStorageLocator;
 		this.repository = repository;
@@ -170,7 +182,7 @@ public class ProjectFileManager implements ProjectData {
 	 * @param versionedFileSystem an existing versioned file-system
 	 * @throws IOException if an IO error occurs
 	 */
-	ProjectFileManager(LocalFileSystem fileSystem, FileSystem versionedFileSystem)
+	DefaultProjectData(LocalFileSystem fileSystem, FileSystem versionedFileSystem)
 			throws IOException {
 		this.localStorageLocator = new ProjectLocator(null, "Test");
 		owner = SystemUtilities.getUserName();
@@ -530,7 +542,7 @@ public class ProjectFileManager implements ProjectData {
 
 	/**
 	 * Returns the owner of the project that is associated with this 
-	 * ProjectFileManager.  A value of null indicates an old multiuser
+	 * DefaultProjectData.  A value of null indicates an old multiuser
 	 * project.
 	 * @return the owner of the project 
 	 */
@@ -731,8 +743,7 @@ public class ProjectFileManager implements ProjectData {
 
 	@Override
 	public void updateRepositoryInfo(RepositoryAdapter newRepository, boolean force,
-			TaskMonitor monitor)
-			throws IOException, CancelledException {
+			TaskMonitor monitor) throws IOException, CancelledException {
 
 		newRepository.connect();
 		if (!newRepository.isConnected()) {
@@ -761,8 +772,8 @@ public class ProjectFileManager implements ProjectData {
 			long checkoutId = item.getCheckoutId();
 			int checkoutVersion = item.getCheckoutVersion();
 
-			ItemCheckoutStatus otherCheckoutStatus = newRepository.getCheckout(
-				df.getParent().getPathname(), df.getName(), checkoutId);
+			ItemCheckoutStatus otherCheckoutStatus =
+				newRepository.getCheckout(df.getParent().getPathname(), df.getName(), checkoutId);
 
 			if (!newRepository.getUser().getName().equals(otherCheckoutStatus.getUser())) {
 				return true;
@@ -793,6 +804,7 @@ public class ProjectFileManager implements ProjectData {
 	 * @throws IOException if IO error occurs
 	 * @throws CancelledException if task cancelled
 	 */
+	@Override
 	public boolean hasInvalidCheckouts(List<DomainFile> checkoutList,
 			RepositoryAdapter newRepository, TaskMonitor monitor)
 			throws IOException, CancelledException {
@@ -856,6 +868,7 @@ public class ProjectFileManager implements ProjectData {
 	 * @throws IOException if IO error occurs
 	 * @throws CancelledException if task cancelled
 	 */
+	@Override
 	public List<DomainFile> findCheckedOutFiles(TaskMonitor monitor)
 			throws IOException, CancelledException {
 		List<DomainFile> list = new ArrayList<>();
@@ -864,8 +877,7 @@ public class ProjectFileManager implements ProjectData {
 	}
 
 	private void findCheckedOutFiles(String folderPath, List<DomainFile> checkoutList,
-			TaskMonitor monitor)
-			throws IOException, CancelledException {
+			TaskMonitor monitor) throws IOException, CancelledException {
 
 		for (String name : fileSystem.getItemNames(folderPath)) {
 			monitor.checkCancelled();
@@ -902,6 +914,30 @@ public class ProjectFileManager implements ProjectData {
 		}
 	}
 
+	@Override
+	public URL getSharedProjectURL() {
+		URL projectURL = localStorageLocator.getURL();
+		if (!GhidraURL.isServerRepositoryURL(projectURL)) {
+			if (repository == null) {
+				return null;
+			}
+			// NOTE: only supports ghidra protocol without extension protocol.
+			// Assumes any extension protocol use would be reflected in ProjectLocator URL.
+			ServerInfo serverInfo = repository.getServerInfo();
+			projectURL = GhidraURL.makeURL(serverInfo.getServerName(), serverInfo.getPortNumber(),
+				repository.getName());
+		}
+		return projectURL;
+	}
+
+	@Override
+	public URL getLocalProjectURL() {
+		if (!localStorageLocator.isTransient()) {
+			return localStorageLocator.getURL();
+		}
+		return null;
+	}
+
 	/**
 	 * Returns the standard user data filename associated with the specified file ID.
 	 * @param associatedFileID the file id
@@ -934,7 +970,7 @@ public class ProjectFileManager implements ProjectData {
 		}
 
 		userDataReconcileTimer = new GhidraSwinglessTimer(USER_DATA_RECONCILE_DELAY_MS, () -> {
-			synchronized (ProjectFileManager.this) {
+			synchronized (DefaultProjectData.this) {
 				startReconcileUserDataFiles();
 			}
 		});
@@ -1184,14 +1220,64 @@ public class ProjectFileManager implements ProjectData {
 		return projectDir;
 	}
 
+	public synchronized boolean isClosed() {
+		return closed;
+	}
+
+	public synchronized boolean isDisposed() {
+		return disposed;
+	}
+
 	@Override
 	public void close() {
+		synchronized (this) {
+			if (!closed) {
+				Msg.debug(this, "Closing ProjectData: " + projectDir);
+				closed = true;
+			}
+			if (inUseCount != 0) {
+				return; // delay dispose
+			}
+		}
 		dispose();
 	}
 
-	public void dispose() {
+	private synchronized void incrementInUseCount() {
+		++inUseCount;
+	}
+
+	private void decrementInUseCount() {
+		synchronized (this) {
+			if (inUseCount <= 0) {
+				Msg.error(this, "DefaultProjectData in-use tracking is out-of-sync: " + projectDir);
+			}
+			if (--inUseCount > 0 || !closed) {
+				return;
+			}
+		}
+		dispose();
+	}
+
+	/**
+	 * Immediately dispose this project data store instance.  If this project has an associated
+	 * {@link RepositoryAdapter} it will be disconnected as well.  This method should generally not
+	 * be used directly when there may be open {@link DomainObject} instances which may rely
+	 * on an associated server connection.  The {@link #clone()} method should be used when
+	 * open {@link DomainObject} instances may exist and should be allowed to persist until
+	 * they are closed.
+	 */
+	protected void dispose() {
 
 		synchronized (this) {
+			if (disposed) {
+				return;
+			}
+
+			Msg.debug(this, "Disposing ProjectData: " + projectDir);
+
+			closed = true;
+			disposed = true;
+
 			if (userDataReconcileTimer != null) {
 				userDataReconcileTimer.stop();
 			}
@@ -1255,7 +1341,7 @@ public class ProjectFileManager implements ProjectData {
 	/**
 	 * Returns the open domain object (opened for update) for the specified path.
 	 * @param pathname the path name
-	 * @return the domain object
+	 * @return the domain object or null if not open
 	 */
 	synchronized DomainObjectAdapter getOpenedDomainObject(String pathname) {
 		return openDomainObjects.get(pathname);
@@ -1298,4 +1384,55 @@ public class ProjectFileManager implements ProjectData {
 	public TaskMonitor getProjectDisposalMonitor() {
 		return projectDisposalMonitor;
 	}
+
+	/**
+	 * Signals the start of a complex merge operation.
+	 * The {@link #mergeEnded()} must be invoked after this method invocation when the
+	 * merge operation has completed.
+	 */
+	void mergeStarted() {
+		incrementInUseCount();
+	}
+
+	/**
+	 * Signals the completion of a complex merge operation (see {@link #mergeStarted()}).
+	 */
+	void mergeEnded() {
+		decrementInUseCount();
+	}
+
+	/**
+	 * Signals that a <b>non-link</b> file has been opened as the specified 
+	 * {@link DomainObjectAdapter doa} from this project data store and should be
+	 * tracked.  This will delay disposal of this object until the specified domain object is
+	 * either closed or saved to a different project store (i.e., hand-off operation).
+	 * It is important that this method not be invoked when opening a link-file
+	 * since it is the referenced file being opened that must be tracked and not the 
+	 * opening of the link-file itself.
+	 * @param doa domain object
+	 */
+	void trackDomainFileInUse(DomainObjectAdapter doa) {
+		DefaultProjectData projectData = fileTrackingMap.put(doa, this);
+		if (projectData == this) {
+			return; // no change in associated project
+		}
+
+		if (projectData != null) {
+			projectData.decrementInUseCount();
+		}
+		else {
+			doa.addCloseListener(dobj -> domainObjectClosed(dobj));
+		}
+
+		incrementInUseCount();
+	}
+
+	private static void domainObjectClosed(DomainObject dobj) {
+
+		DefaultProjectData projectData = fileTrackingMap.remove(dobj);
+		if (projectData != null) {
+			projectData.decrementInUseCount();
+		}
+	}
+
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DomainFileIndex.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -29,10 +28,10 @@ import java.util.HashMap;
  */
 class DomainFileIndex implements DomainFolderChangeListener {
 
-	private ProjectFileManager projectData;
+	private DefaultProjectData projectData;
 	private HashMap<String, String> fileIdToPathIndex = new HashMap<String, String>();
 
-	DomainFileIndex(ProjectFileManager projectData) {
+	DomainFileIndex(DefaultProjectData projectData) {
 		this.projectData = projectData;
 	}
 

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DomainFileProxy.java

@@ -23,14 +23,11 @@ import java.util.*;
 
 import javax.swing.Icon;
 
-import org.apache.commons.lang3.StringUtils;
-
 import ghidra.framework.client.*;
 import ghidra.framework.model.*;
 import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.remote.RepositoryItem;
-import ghidra.framework.store.ItemCheckoutStatus;
-import ghidra.framework.store.Version;
+import ghidra.framework.store.*;
 import ghidra.framework.store.db.PackedDatabase;
 import ghidra.util.InvalidNameException;
 import ghidra.util.ReadOnlyException;
@@ -120,11 +117,13 @@ public class DomainFileProxy implements DomainFile {
 
 	private URL getSharedFileURL(URL sharedProjectURL, String ref) {
 		try {
-			String spec = getPathname().substring(1); // remove leading '/'
-			if (!StringUtils.isEmpty(ref)) {
-				spec += "#" + ref;
+			// Direct URL construction done so that ghidra protocol extension may be supported
+			String urlStr = sharedProjectURL.toExternalForm();
+			if (urlStr.endsWith(FileSystem.SEPARATOR)) {
+				urlStr = urlStr.substring(0, urlStr.length() - 1);
 			}
-			return new URL(sharedProjectURL, spec);
+			urlStr += getPathname();
+			return new URL(urlStr);
 		}
 		catch (MalformedURLException e) {
 			// ignore
@@ -136,12 +135,12 @@ public class DomainFileProxy implements DomainFile {
 		if (properties == null) {
 			return null;
 		}
-		String serverName = properties.getProperty(ProjectFileManager.SERVER_NAME);
-		String repoName = properties.getProperty(ProjectFileManager.REPOSITORY_NAME);
+		String serverName = properties.getProperty(DefaultProjectData.SERVER_NAME);
+		String repoName = properties.getProperty(DefaultProjectData.REPOSITORY_NAME);
 		if (serverName == null || repoName == null) {
 			return null;
 		}
-		int port = Integer.parseInt(properties.getProperty(ProjectFileManager.PORT_NUMBER, "0"));
+		int port = Integer.parseInt(properties.getProperty(DefaultProjectData.PORT_NUMBER, "0"));
 
 		if (!ClientUtil.isConnected(serverName, port)) {
 			return null; // avoid initiating a server connection. 
@@ -187,7 +186,7 @@ public class DomainFileProxy implements DomainFile {
 				return getSharedFileURL(projectURL, ref);
 			}
 			Properties properties =
-				ProjectFileManager.readProjectProperties(projectLocation.getProjectDir());
+				DefaultProjectData.readProjectProperties(projectLocation.getProjectDir());
 			return getSharedFileURL(properties, ref);
 		}
 		return null;

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/DomainObjectAdapter.java

@@ -54,8 +54,7 @@ public abstract class DomainObjectAdapter implements DomainObject {
 	protected Map<EventQueueID, DomainObjectChangeSupport> changeSupportMap =
 		new ConcurrentHashMap<EventQueueID, DomainObjectChangeSupport>();
 	private volatile boolean eventsEnabled = true;
-	private Set<DomainObjectClosedListener> closeListeners =
-		new CopyOnWriteArraySet<DomainObjectClosedListener>();
+	private Set<DomainObjectClosedListener> closeListeners = new CopyOnWriteArraySet<>();
 
 	private ArrayList<Object> consumers;
 	protected Map<String, String> metadata = new LinkedHashMap<String, String>();
@@ -210,7 +209,7 @@ public abstract class DomainObjectAdapter implements DomainObject {
 
 	private void notifyCloseListeners() {
 		for (DomainObjectClosedListener listener : closeListeners) {
-			listener.domainObjectClosed();
+			listener.domainObjectClosed(this);
 		}
 		closeListeners.clear();
 	}

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/GhidraFile.java

@@ -33,7 +33,7 @@ public class GhidraFile implements DomainFile {
 
 	// FIXME: This implementation assumes a single implementation of the DomainFile and DomainFolder interfaces
 
-	protected ProjectFileManager fileManager;
+	protected DefaultProjectData projectData;
 
 	private LocalFileSystem fileSystem;
 	private DomainFolderChangeListener listener;
@@ -45,13 +45,13 @@ public class GhidraFile implements DomainFile {
 		this.parent = parent;
 		this.name = name;
 
-		this.fileManager = parent.getProjectFileManager();
+		this.projectData = parent.getProjectData();
 		this.fileSystem = parent.getLocalFileSystem();
 		this.listener = parent.getChangeListener();
 	}
 
 	public LocalFileSystem getUserFileSystem() {
-		return fileManager.getUserFileSystem();
+		return projectData.getUserFileSystem();
 	}
 
 	private GhidraFileData getFileData() throws FileNotFoundException, IOException {
@@ -97,8 +97,8 @@ public class GhidraFile implements DomainFile {
 
 	void clearDomainObj() {
 		String path = getPathname();
-		DomainObjectAdapter doa = fileManager.getOpenedDomainObject(path);
-		if (doa != null && fileManager.clearDomainObject(getPathname())) {
+		DomainObjectAdapter doa = projectData.getOpenedDomainObject(path);
+		if (doa != null && projectData.clearDomainObject(getPathname())) {
 			listener.domainFileObjectClosed(this, doa);
 		}
 	}
@@ -120,7 +120,7 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public ProjectLocator getProjectLocator() {
-		return fileManager.getProjectLocator();
+		return projectData.getProjectLocator();
 	}
 
 	@Override
@@ -215,10 +215,10 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public DomainObject getOpenedDomainObject(Object consumer) {
-		DomainObjectAdapter domainObj = fileManager.getOpenedDomainObject(getPathname());
+		DomainObjectAdapter domainObj = projectData.getOpenedDomainObject(getPathname());
 		if (domainObj != null) {
 			if (!domainObj.addConsumer(consumer)) {
-				fileManager.clearDomainObject(getPathname());
+				projectData.clearDomainObject(getPathname());
 				throw new IllegalStateException("Domain Object is closed: " + domainObj.getName());
 			}
 		}
@@ -248,7 +248,7 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public void save(TaskMonitor monitor) throws IOException, CancelledException {
-		DomainObjectAdapter dobj = fileManager.getOpenedDomainObject(getPathname());
+		DomainObjectAdapter dobj = projectData.getOpenedDomainObject(getPathname());
 		if (dobj == null) {
 			throw new AssertException("Cannot save, domainObj not open");
 		}
@@ -263,7 +263,7 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public boolean canSave() {
-		DomainObjectAdapter dobj = fileManager.getOpenedDomainObject(getPathname());
+		DomainObjectAdapter dobj = projectData.getOpenedDomainObject(getPathname());
 		if (dobj == null) {
 			return false;
 		}
@@ -573,7 +573,7 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public ArrayList<?> getConsumers() {
-		DomainObjectAdapter dobj = fileManager.getOpenedDomainObject(getPathname());
+		DomainObjectAdapter dobj = projectData.getOpenedDomainObject(getPathname());
 		if (dobj == null) {
 			return new ArrayList<>();
 		}
@@ -582,13 +582,13 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public boolean isChanged() {
-		DomainObjectAdapter dobj = fileManager.getOpenedDomainObject(getPathname());
+		DomainObjectAdapter dobj = projectData.getOpenedDomainObject(getPathname());
 		return dobj != null && dobj.isChanged();
 	}
 
 	@Override
 	public boolean isOpen() {
-		return fileManager.getOpenedDomainObject(getPathname()) != null;
+		return projectData.getOpenedDomainObject(getPathname()) != null;
 	}
 
 	@Override
@@ -640,7 +640,7 @@ public class GhidraFile implements DomainFile {
 			return false;
 		}
 		GhidraFile other = (GhidraFile) obj;
-		if (fileManager != other.fileManager) {
+		if (projectData != other.projectData) {
 			return false;
 		}
 		return getPathname().equals(other.getPathname());
@@ -653,11 +653,11 @@ public class GhidraFile implements DomainFile {
 
 	@Override
 	public String toString() {
-		ProjectLocator projectLocator = parent.getProjectData().getProjectLocator();
+		ProjectLocator projectLocator = projectData.getProjectLocator();
 		if (projectLocator.isTransient()) {
-			return fileManager.getProjectLocator().getName() + getPathname();
+			return projectLocator.getName() + getPathname();
 		}
-		return fileManager.getProjectLocator().getName() + ":" + getPathname();
+		return projectLocator.getName() + ":" + getPathname();
 	}
 
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/GhidraFolder.java

@@ -20,7 +20,6 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.List;
 
-import ghidra.framework.client.RepositoryAdapter;
 import ghidra.framework.model.*;
 import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.store.FileSystem;
@@ -32,7 +31,7 @@ import ghidra.util.task.TaskMonitor;
 
 public class GhidraFolder implements DomainFolder {
 
-	private ProjectFileManager fileManager;
+	private DefaultProjectData projectData;
 	private LocalFileSystem fileSystem;
 	private FileSystem versionedFileSystem;
 	private DomainFolderChangeListener listener;
@@ -40,10 +39,10 @@ public class GhidraFolder implements DomainFolder {
 	private GhidraFolder parent;
 	private String name;
 
-	GhidraFolder(ProjectFileManager fileManager, DomainFolderChangeListener listener) {
-		this.fileManager = fileManager;
-		this.fileSystem = fileManager.getLocalFileSystem();
-		this.versionedFileSystem = fileManager.getVersionedFileSystem();
+	GhidraFolder(DefaultProjectData projectData, DomainFolderChangeListener listener) {
+		this.projectData = projectData;
+		this.fileSystem = projectData.getLocalFileSystem();
+		this.versionedFileSystem = projectData.getVersionedFileSystem();
 		this.listener = listener;
 		this.name = FileSystem.SEPARATOR;
 	}
@@ -52,7 +51,7 @@ public class GhidraFolder implements DomainFolder {
 		this.parent = parent;
 		this.name = name;
 
-		this.fileManager = parent.getProjectFileManager();
+		this.projectData = parent.getProjectData();
 		this.fileSystem = parent.getLocalFileSystem();
 		this.versionedFileSystem = parent.getVersionedFileSystem();
 		this.listener = parent.getChangeListener();
@@ -67,17 +66,13 @@ public class GhidraFolder implements DomainFolder {
 	}
 
 	LocalFileSystem getUserFileSystem() {
-		return fileManager.getUserFileSystem();
+		return projectData.getUserFileSystem();
 	}
 
 	DomainFolderChangeListener getChangeListener() {
 		return listener;
 	}
 
-	ProjectFileManager getProjectFileManager() {
-		return fileManager;
-	}
-
 	GhidraFileData getFileData(String fileName) throws FileNotFoundException, IOException {
 		GhidraFileData fileData = getFolderData().getFileData(fileName, false);
 		if (fileData == null) {
@@ -88,7 +83,7 @@ public class GhidraFolder implements DomainFolder {
 
 	GhidraFolderData getFolderData() throws FileNotFoundException {
 		if (parent == null) {
-			return fileManager.getRootFolderData();
+			return projectData.getRootFolderData();
 		}
 		GhidraFolderData folderData = parent.getFolderData().getFolderData(name, false);
 		if (folderData == null) {
@@ -106,7 +101,7 @@ public class GhidraFolder implements DomainFolder {
 	private GhidraFolderData createFolderData(String folderName) throws IOException {
 		synchronized (fileSystem) {
 			GhidraFolderData parentData =
-				parent == null ? fileManager.getRootFolderData() : createFolderData();
+				parent == null ? projectData.getRootFolderData() : createFolderData();
 			GhidraFolderData folderData = parentData.getFolderData(folderName, false);
 			if (folderData == null) {
 				try {
@@ -121,7 +116,7 @@ public class GhidraFolder implements DomainFolder {
 	}
 
 	private GhidraFolderData createFolderData() throws IOException {
-		GhidraFolderData rootFolderData = fileManager.getRootFolderData();
+		GhidraFolderData rootFolderData = projectData.getRootFolderData();
 		if (parent == null) {
 			return rootFolderData;
 		}
@@ -153,12 +148,12 @@ public class GhidraFolder implements DomainFolder {
 
 	@Override
 	public ProjectLocator getProjectLocator() {
-		return fileManager.getProjectLocator();
+		return projectData.getProjectLocator();
 	}
 
 	@Override
-	public ProjectFileManager getProjectData() {
-		return fileManager;
+	public DefaultProjectData getProjectData() {
+		return projectData;
 	}
 
 	String getPathname(String childName) {
@@ -185,19 +180,10 @@ public class GhidraFolder implements DomainFolder {
 
 	@Override
 	public URL getSharedProjectURL() {
-		ProjectLocator projectLocator = getProjectLocator();
-		URL projectURL = projectLocator.getURL();
-		if (!GhidraURL.isServerRepositoryURL(projectURL)) {
-			RepositoryAdapter repository = fileManager.getRepository();
-			if (repository == null) {
+		URL projectURL = projectData.getSharedProjectURL();
+		if (projectURL == null) {
 			return null;
 		}
-			// NOTE: only supports ghidra protocol without extension protocol.
-			// Assumes any extension protocol use would be reflected in projectLocator URL.
-			ServerInfo serverInfo = repository.getServerInfo();
-			projectURL = GhidraURL.makeURL(serverInfo.getServerName(), serverInfo.getPortNumber(),
-				repository.getName());
-		}
 		try {
 			// Direct URL construction done so that ghidra protocol extension may be supported
 			String urlStr = projectURL.toExternalForm();
@@ -218,7 +204,7 @@ public class GhidraFolder implements DomainFolder {
 
 	@Override
 	public URL getLocalProjectURL() {
-		ProjectLocator projectLocator = parent.getProjectLocator();
+		ProjectLocator projectLocator = projectData.getProjectLocator();
 		if (!projectLocator.isTransient()) {
 			return GhidraURL.makeURL(projectLocator, getPathname(), null);
 		}
@@ -227,7 +213,7 @@ public class GhidraFolder implements DomainFolder {
 
 	@Override
 	public boolean isInWritableProject() {
-		return !getProjectData().getLocalFileSystem().isReadOnly();
+		return !fileSystem.isReadOnly();
 	}
 
 	@Override
@@ -319,7 +305,7 @@ public class GhidraFolder implements DomainFolder {
 				}
 			}
 			catch (IOException e) {
-				Msg.error(this, "file error for " + parent.getPathname(fileName), e);
+				Msg.error(this, "file error for " + getPathname(fileName), e);
 			}
 			return null;
 		}
@@ -424,7 +410,7 @@ public class GhidraFolder implements DomainFolder {
 			return false;
 		}
 		GhidraFolder other = (GhidraFolder) obj;
-		if (fileManager != other.fileManager) {
+		if (projectData != other.projectData) {
 			return false;
 		}
 		return getPathname().equals(other.getPathname());
@@ -437,11 +423,11 @@ public class GhidraFolder implements DomainFolder {
 
 	@Override
 	public String toString() {
-		ProjectLocator projectLocator = fileManager.getProjectLocator();
+		ProjectLocator projectLocator = projectData.getProjectLocator();
 		if (projectLocator.isTransient()) {
-			return fileManager.getProjectLocator().getName() + getPathname();
+			return projectData.getProjectLocator().getName() + getPathname();
 		}
-		return fileManager.getProjectLocator().getName() + ":" + getPathname();
+		return projectData.getProjectLocator().getName() + ":" + getPathname();
 	}
 
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/GhidraFolderData.java

@@ -24,14 +24,25 @@ import ghidra.framework.model.*;
 import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.framework.protocol.ghidra.TransientProjectData;
 import ghidra.framework.store.FileSystem;
+import ghidra.framework.store.FolderNotEmptyException;
 import ghidra.framework.store.local.LocalFileSystem;
 import ghidra.util.*;
 import ghidra.util.exception.*;
 import ghidra.util.task.TaskMonitor;
 
+/**
+ * {@link GhidraFolderData} provides the managed object which represents a project folder that 
+ * corresponds to matched folder paths across both a versioned and private 
+ * filesystem and viewed as a single folder at the project level.  This class closely mirrors the
+ * {@link DomainFolder} interface and is used by the {@link GhidraFolder} implementation; both of which
+ * represent immutable folder references.  Changes made to this folder's name or path are not reflected 
+ * in old {@link DomainFolder} instances and must be re-instantiated following such a change.  
+ * Any long-term retention of {@link DomainFolder} and {@link DomainFile} instances requires an 
+ * appropriate change listener to properly discard/reacquire such instances.
+ */
 class GhidraFolderData {
 
-	private ProjectFileManager fileManager;
+	private DefaultProjectData projectData;
 
 	/**
 	 * Folder change listener - change events only sent if folder is visited
@@ -59,17 +70,24 @@ class GhidraFolderData {
 	private boolean versionedFolderExists;
 
 	/**
-	 * General constructor reserved for root folder use only
-	 * @param fileManager
-	 * @param listener
+	 * General constructor reserved for root folder instantiation
+	 * @param projectData associated project data instance
+	 * @param listener folder change listener
 	 */
-	GhidraFolderData(ProjectFileManager fileManager, DomainFolderChangeListener listener) {
-		this.fileManager = fileManager;
-		this.fileSystem = fileManager.getLocalFileSystem();
-		this.versionedFileSystem = fileManager.getVersionedFileSystem();
+	GhidraFolderData(DefaultProjectData projectData, DomainFolderChangeListener listener) {
+		this.projectData = projectData;
+		this.fileSystem = projectData.getLocalFileSystem();
+		this.versionedFileSystem = projectData.getVersionedFileSystem();
 		this.listener = listener;
 	}
 
+	/**
+	 * Construct a folder instance with a specified name and a correpsonding parent folder
+	 * @param parent parent folder
+	 * @param name folder name
+	 * @throws FileNotFoundException if folder not found or error occured while checking
+	 * for its existance
+	 */
 	GhidraFolderData(GhidraFolderData parent, String name) throws FileNotFoundException {
 		if (name == null || name.isEmpty()) {
 			throw new FileNotFoundException("Bad folder name: blank or null");
@@ -77,7 +95,7 @@ class GhidraFolderData {
 		this.parent = parent;
 		this.name = name;
 
-		this.fileManager = parent.getProjectFileManager();
+		this.projectData = parent.getProjectData();
 		this.fileSystem = parent.getLocalFileSystem();
 		this.versionedFileSystem = parent.getVersionedFileSystem();
 		this.listener = parent.getChangeListener();
@@ -95,36 +113,59 @@ class GhidraFolderData {
 	}
 
 	/**
-	 * Returns true if folder has complete list of children
+	 * @return true if folder has complete list of children
 	 */
 	boolean visited() {
 		return visited;
 	}
 
+	/**
+	 * @return local file system
+	 */
 	LocalFileSystem getLocalFileSystem() {
 		return fileSystem;
 	}
 
+	/**
+	 * @return versioned file system
+	 */
 	FileSystem getVersionedFileSystem() {
 		return versionedFileSystem;
 	}
 
+	/**
+	 * @return local user data file system
+	 */
 	LocalFileSystem getUserFileSystem() {
-		return fileManager.getUserFileSystem();
+		return projectData.getUserFileSystem();
 	}
 
+	/**
+	 * @return folder change listener
+	 */
 	DomainFolderChangeListener getChangeListener() {
 		return listener;
 	}
 
-	ProjectFileManager getProjectFileManager() {
-		return fileManager;
+	/**
+	 * @return project data instance
+	 */
+	DefaultProjectData getProjectData() {
+		return projectData;
 	}
 
+	/**
+	 * Get the project locator which identifies the system storage
+	 * are for the local file system and other project related resources.
+	 * @return local project locator
+	 */
 	ProjectLocator getProjectLocator() {
-		return fileManager.getProjectLocator();
+		return projectData.getProjectLocator();
 	}
 
+	/**
+	 * @return this folder's parent folder or null if this is the root folder.
+	 */
 	GhidraFolderData getParentData() {
 		return parent;
 	}
@@ -143,7 +184,7 @@ class GhidraFolderData {
 			}
 		}
 		else if (folderPath.startsWith(FileSystem.SEPARATOR)) {
-			return fileManager.getRootFolderData().getFolderPathData(folderPath, lazy);
+			return projectData.getRootFolderData().getFolderPathData(folderPath, lazy);
 		}
 		if (folderPath.length() == 0) {
 			return this;
@@ -168,10 +209,26 @@ class GhidraFolderData {
 		return folderData.getFolderPathData(nextPath, lazy);
 	}
 
+	/**
+	 * Return this folder's name.
+	 * @return the name
+	 */
 	String getName() {
 		return name;
 	}
 
+	/**
+	 * Set the name on this domain folder.
+	 * @param newName domain folder name
+	 * @return renamed domain file (the original DomainFolder object becomes invalid since it is 
+	 * immutable)
+	 * @throws InvalidNameException if newName contains illegal characters
+	 * @throws DuplicateFileException if a folder named newName 
+	 * already exists in this files domain folder.
+	 * @throws FileInUseException if any file within this folder or its descendants is 
+	 * in-use / checked-out.
+	 * @throws IOException thrown if an IO or access error occurs.
+	 */
 	GhidraFolder setName(String newName) throws InvalidNameException, IOException {
 		synchronized (fileSystem) {
 			if (parent == null || fileSystem.isReadOnly()) {
@@ -242,6 +299,10 @@ class GhidraFolderData {
 		return path;
 	}
 
+	/**
+	 * Returns the full path name to this folder
+	 * @return the path name
+	 */
 	String getPathname() {
 		if (parent == null) {
 			return FileSystem.SEPARATOR;
@@ -254,6 +315,10 @@ class GhidraFolderData {
 		return path;
 	}
 
+	/**
+	 * Determine if this folder contains any sub-folders or domain files.
+	 * @return true if this folder is empty.
+	 */
 	boolean isEmpty() {
 		try {
 			refresh(false, false, null); // visited will be true upon return
@@ -266,6 +331,10 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Get the list of names for all files contained within this folder.
+	 * @return list of file names
+	 */
 	List<String> getFileNames() {
 		try {
 			refresh(false, false, null); // visited will be true upon return
@@ -277,6 +346,10 @@ class GhidraFolderData {
 		return new ArrayList<>(fileList);
 	}
 
+	/**
+	 * Get the list of names for all subfolders contained within this folder.
+	 * @return list of file names
+	 */
 	List<String> getFolderNames() {
 		try {
 			refresh(false, false, null); // visited will be true upon return
@@ -289,9 +362,10 @@ class GhidraFolderData {
 	}
 
 	/**
-	 * Update file list/cache based upon rename of file.
-	 * If this folder has been visited listener will be notified with rename
-	 * @param oldName
+	 * Update file list/cache based upon rename of a file.
+	 * If this folder has been visited the listener will be notified with rename
+	 * @param oldFileName file name prior to rename
+	 * @param newFileName file name after rename
 	 */
 	void fileRenamed(String oldFileName, String newFileName) {
 		GhidraFileData fileData;
@@ -314,6 +388,14 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Update file list/cache based upon change of parent for a file.
+	 * If this folder or the newParent has been visited the listener will be notified with add/move
+	 * details.
+	 * @param newParent new parent folder
+	 * @param oldFileName file name prior to move
+	 * @param newFileName file name after move
+	 */
 	void fileMoved(GhidraFolderData newParent, String oldFileName, String newFileName) {
 		GhidraFileData fileData;
 		synchronized (fileSystem) {
@@ -340,7 +422,7 @@ class GhidraFolderData {
 	 * underlying local or versioned file.  If this folder has been visited an appropriate
 	 * add/remove/change notification will be provided to the listener.
 	 * NOTE: Move and Rename situations are not handled
-	 * @param fileName
+	 * @param fileName name of file which has changed
 	 */
 	void fileChanged(String fileName) {
 		synchronized (fileSystem) {
@@ -389,7 +471,8 @@ class GhidraFolderData {
 	 * visited an appropriate add/remove/change notification will be provided to the listener.  
 	 * NOTE: Care should be taken using this method as all sub-folder cache data may be disposed!
 	 * NOTE: Move and Rename situations are not handled
-	 * @param folderName
+	 * @param folderName name of folder which has changed
+	 * @throws IOException if an IO error occurs during associated refresh
 	 */
 	void folderChanged(String folderName) throws IOException {
 		synchronized (fileSystem) {
@@ -404,7 +487,7 @@ class GhidraFolderData {
 				if (folderData.versionedFolderExists || folderData.folderExists) {
 					// preserve subfolder data
 					if (folderData.visited) {
-						folderData.refresh(true, true, fileManager.getProjectDisposalMonitor());
+						folderData.refresh(true, true, projectData.getProjectDisposalMonitor());
 					}
 					return;
 				}
@@ -429,7 +512,7 @@ class GhidraFolderData {
 	/**
 	 * Remove and dispose specified subfolder data and notify listener of removal
 	 * if this folder has been visited
-	 * @param folderName
+	 * @param folderName name of folder which was removed
 	 */
 	void folderRemoved(String folderName) {
 		synchronized (fileSystem) {
@@ -443,6 +526,9 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Disposes the cached data for this folder and all of its children recursively.
+	 */
 	void dispose() {
 		visited = false;
 		folderList.clear();
@@ -458,7 +544,7 @@ class GhidraFolderData {
 // NOTE: clearing the following can cause issues since there may be some residual 
 // activity/use which will get a NPE
 //		parent = null;
-//		fileManager = null;
+//		projectData = null;
 //		listener = null;
 	}
 
@@ -476,7 +562,7 @@ class GhidraFolderData {
 	 * Refresh set of sub-folder names and identify added/removed folders.
 	 * @param recursive recurse into visited subfolders if true
 	 * @param monitor recursion task monitor - break from recursion if cancelled
-	 * @throws IOException
+	 * @throws IOException if an IO error occurs during the refresh
 	 */
 	private void refreshFolders(boolean recursive, TaskMonitor monitor) throws IOException {
 
@@ -653,7 +739,7 @@ class GhidraFolderData {
 	 * of visited state, if false refresh is lazy and will not be 
 	 * performed if a previous refresh set the visited state.
 	 * @param monitor recursion task monitor - break from recursion if cancelled
-	 * @throws IOException
+	 * @throws IOException if an IO error occurs during the refresh
 	 */
 	void refresh(boolean recursive, boolean force, TaskMonitor monitor) throws IOException {
 		synchronized (fileSystem) {
@@ -699,11 +785,11 @@ class GhidraFolderData {
 	}
 
 	/**
-	 * Check for existence of subfolder.  If this folder visited, rely on folderList
-	 * @param fileName
-	 * @param doRealCheck if true do not rely on fileList
-	 * @return
-	 * @throws IOException
+	 * Check for existence of subfolder.  If this folder has previously been visited, 
+	 * rely on the cached folderList.
+	 * @param folderName name of folder to look for
+	 * @return true if folder exists, else false
+	 * @throws IOException if an IO error occurs when checking for folder's existance.
 	 */
 	boolean containsFolder(String folderName) throws IOException {
 		synchronized (fileSystem) {
@@ -720,8 +806,8 @@ class GhidraFolderData {
 	/**
 	 * Create and add new subfolder data object to cache.  Data will not be created
 	 * if folder does not exist or an IOException occurs.
-	 * @param folderName
-	 * @return folder data or null
+	 * @param folderName name of folder to be added
+	 * @return folder data or null if folder does not exist
 	 */
 	private GhidraFolderData addFolderData(String folderName) {
 		GhidraFolderData folderData = folderDataCache.get(folderName);
@@ -739,7 +825,7 @@ class GhidraFolderData {
 
 	/**
 	 * Get folder data for child folder specified by folderName
-	 * @param folderName
+	 * @param folderName name of folder
 	 * @param lazy if true folder will not be searched for if not already discovered - in
 	 * this case null will be returned
 	 * @return folder data or null if not found or lazy=true and not yet discovered
@@ -763,10 +849,10 @@ class GhidraFolderData {
 	}
 
 	/**
-	 * Check for existence of file.  If folder visited, rely on fileDataCache
-	 * @param fileName the name of the file to check for
-	 * @return true if this folder contains the fileName
-	 * @throws IOException
+	 * Check for existence of file.  If folder previously visited, rely on fileDataCache
+	 * @param fileName the name of the file to look for
+	 * @return true if this folder contains the fileName, else false
+	 * @throws IOException if an IO error occurs while checking for file existance
 	 */
 	public boolean containsFile(String fileName) throws IOException {
 		synchronized (fileSystem) {
@@ -783,9 +869,9 @@ class GhidraFolderData {
 	/**
 	 * Create and add new file data object to cache.  Data will not be created
 	 * if file does not exist or an IOException occurs.
-	 * @param fileName
-	 * @return file data or null
-	 * @throws IOException
+	 * @param fileName name of file
+	 * @return file data or null if not found
+	 * @throws IOException if an IO error occurs while checking for file existance
 	 */
 	private GhidraFileData addFileData(String fileName) throws IOException {
 		GhidraFileData fileData = fileDataCache.get(fileName);
@@ -793,7 +879,7 @@ class GhidraFolderData {
 			try {
 				fileData = new GhidraFileData(this, fileName);
 				fileDataCache.put(fileName, fileData);
-				fileManager.updateFileIndex(fileData);
+				projectData.updateFileIndex(fileData);
 			}
 			catch (FileNotFoundException e) {
 				// ignore
@@ -804,10 +890,11 @@ class GhidraFolderData {
 
 	/**
 	 * Get file data for child specified by fileName
-	 * @param fileName
+	 * @param fileName name of file
 	 * @param lazy if true file will not be searched for if not already discovered - in
 	 * this case null will be returned
 	 * @return file data or null if not found or lazy=true and not yet discovered
+	 * @throws IOException if an IO error occurs while checking for file existance
 	 */
 	GhidraFileData getFileData(String fileName, boolean lazy) throws IOException {
 		synchronized (fileSystem) {
@@ -822,58 +909,11 @@ class GhidraFolderData {
 		return null;
 	}
 
-//	// TODO: Examine!
-//	private void removeFolderX(String folderName) {
-//		folderList.remove(folderName);
-//		folderDataCache.remove(folderName);
-//		listener.domainFolderRemoved(getDomainFolder(), folderName);
-//	}
-//
-//	// TODO: Examine!
-//	void removeFileX(String fileName) {
-//		fileList.remove(fileName);
-//		GhidraFileV2Data fileData = fileDataCache.remove(fileName);
-//		if (fileData != null) {
-//			fileData.dispose();
-//		}
-//// TODO: May need to eliminate presence of fileID in callback
-//		listener.domainFileRemoved(getDomainFolder(), fileName, null /* fileID */);
-//	}
-//
-//	/**
-//	 * Handle addition of new file.  If this folder has been visited, listener
-//	 * will be notified of new file addition or change
-//	 * @param fileName
-//	 * @return
-//	 */
-//	// TODO: Examine!
-//	GhidraFile fileAddedX(String fileName) {
-//		invalidateFile(fileName);
-//		GhidraFile df = getDomainFile(fileName);
-//		if (visited) {
-//			getFileData(fileName, false);
-//			if (fileList.add(fileName)) {
-//				listener.domainFileAdded(df);
-//			}
-//			else {
-//				listenerX.domainFileStatusChanged(df, fileID)
-//			}
-//		}
-//		return df;
-//	}
-//
-
-//
-//	// TODO: Examine!
-//	private GhidraFolder addFolderX(String folderName) {
-//		invalidateFolder(folderName, false);
-//		GhidraFolder folder = getDomainFolder(folderName);
-//		if (folderList.add(folderName) && visited) {
-//			listener.domainFolderAdded(folder);
-//		}
-//		return folder;
-//	}
-
+	/**
+	 * Get the domain file in this folder with the given fileName.
+	 * @param fileName name of file in this folder to retrieve
+	 * @return domain file or null if there is no file in this folder with the given name.
+	 */
 	GhidraFile getDomainFile(String fileName) {
 		synchronized (fileSystem) {
 			try {
@@ -888,6 +928,11 @@ class GhidraFolderData {
 		return null;
 	}
 
+	/**
+	 * Get the domain folder in this folder with the given subfolderName.
+	 * @param subfolderName name of subfolder in this folder to retrieve
+	 * @return domain folder or null if there is no file in this folder with the given name.
+	 */
 	GhidraFolder getDomainFolder(String subfolderName) {
 		synchronized (fileSystem) {
 			try {
@@ -902,10 +947,26 @@ class GhidraFolderData {
 		return null;
 	}
 
+	/**
+	 * @return a {@link DomainFolder} instance which corresponds to this folder
+	 */
 	GhidraFolder getDomainFolder() {
 		return new GhidraFolder(parent.getDomainFolder(), name);
 	}
 
+	/**
+	 * Add a domain object to this folder.
+	 * @param fileName domain file name
+	 * @param obj domain object to be stored
+	 * @param monitor progress monitor
+	 * @return domain file created as a result of adding
+	 * the domain object to this folder
+	 * @throws DuplicateFileException thrown if the file name already exists
+	 * @throws InvalidNameException if name is an empty string
+	 * or if it contains characters other than alphanumerics.
+	 * @throws IOException if IO or access error occurs
+	 * @throws CancelledException if the user cancels the create.
+	 */
 	GhidraFile createFile(String fileName, DomainObject obj, TaskMonitor monitor)
 			throws InvalidNameException, IOException, CancelledException {
 		synchronized (fileSystem) {
@@ -937,9 +998,12 @@ class GhidraFolderData {
 					throw new IOException("File creation failed for unknown reason");
 				}
 
-				fileManager.setDomainObject(file.getPathname(), doa);
+				projectData.setDomainObject(file.getPathname(), doa);
 				doa.setDomainFile(file);
 				doa.setChanged(false);
+
+				projectData.trackDomainFileInUse(doa);
+
 				listener.domainFileObjectOpenedForUpdate(file, doa);
 
 				return file;
@@ -950,6 +1014,19 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Add a new domain file to this folder.
+	 * @param fileName domain file name
+	 * @param packFile packed file containing domain file data
+	 * @param monitor progress monitor
+	 * @return domain file created as a result of adding
+	 * the domain object to this folder
+	 * @throws DuplicateFileException thrown if the file name already exists
+	 * @throws InvalidNameException if name is an empty string
+	 * or if it contains characters other than alphanumerics.
+	 * @throws IOException if IO or access error occurs
+	 * @throws CancelledException if the user cancels the create.
+	 */
 	GhidraFile createFile(String fileName, File packFile, TaskMonitor monitor)
 			throws InvalidNameException, IOException, CancelledException {
 		synchronized (fileSystem) {
@@ -969,6 +1046,15 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Create a subfolder within this folder.
+	 * @param folderName sub-folder name
+	 * @return the new folder
+	 * @throws DuplicateFileException if a folder by this name already exists
+	 * @throws InvalidNameException if name is an empty string of if it contains characters other 
+	 * than alphanumerics.
+	 * @throws IOException if IO or access error occurs
+	 */
 	GhidraFolderData createFolder(String folderName) throws InvalidNameException, IOException {
 		synchronized (fileSystem) {
 			if (fileSystem.isReadOnly()) {
@@ -984,6 +1070,11 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Deletes this folder, if empty, from the local filesystem
+	 * @throws IOException if IO or access error occurs
+	 * @throws FolderNotEmptyException Thrown if the subfolder is not empty.
+	 */
 	void delete() throws IOException {
 		synchronized (fileSystem) {
 			if (fileSystem.isReadOnly()) {
@@ -1000,6 +1091,9 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Delete this folder from the local filesystem if empty
+	 */
 	void deleteLocalFolderIfEmpty() {
 		synchronized (fileSystem) {
 			try {
@@ -1018,6 +1112,19 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Move this folder into the newParent folder.  If connected to a repository
+	 * this moves both private and repository folders/files.  If not
+	 * connected, only private folders/files are moved.
+	 * @param newParent new parent folder within the same project
+	 * @return the newly relocated folder (the original DomainFolder object becomes invalid since 
+	 * it is immutable)
+	 * @throws DuplicateFileException if a folder with the same name 
+	 * already exists in newParent folder.
+	 * @throws FileInUseException if this folder or one of its descendants 
+	 * contains a file which is in-use / checked-out.
+	 * @throws IOException thrown if an IO or access error occurs.
+	 */
 	GhidraFolder moveTo(GhidraFolderData newParent) throws IOException {
 		synchronized (fileSystem) {
 			if (newParent.getLocalFileSystem() != fileSystem || fileSystem.isReadOnly()) {
@@ -1084,11 +1191,17 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Determine if the specified folder if an ancestor of this folder
+	 * (i.e., parent, grand-parent, etc.).
+	 * @param folderData folder to be checked
+	 * @return true if the specified folder if an ancestor of this folder
+	 */
 	boolean isAncestor(GhidraFolderData folderData) {
-		if (!folderData.fileManager.getProjectLocator().equals(fileManager.getProjectLocator())) {
+		if (!folderData.projectData.getProjectLocator().equals(projectData.getProjectLocator())) {
 			// check if projects share a common repository
-			RepositoryAdapter myRepository = fileManager.getRepository();
-			RepositoryAdapter otherRepository = folderData.fileManager.getRepository();
+			RepositoryAdapter myRepository = projectData.getRepository();
+			RepositoryAdapter otherRepository = folderData.projectData.getRepository();
 			if (myRepository == null || otherRepository == null ||
 				!myRepository.getServerInfo().equals(otherRepository.getServerInfo()) ||
 				!myRepository.getName().equals(otherRepository.getName())) {
@@ -1105,20 +1218,30 @@ class GhidraFolderData {
 		return false;
 	}
 
-	GhidraFolder copyTo(GhidraFolderData newParentData, TaskMonitor monitor)
+	/**
+	 * Copy this folder into the newParent folder.
+	 * @param newParent new parent folder
+	 * @param monitor the task monitor
+	 * @return the new copied folder
+	 * @throws DuplicateFileException if a folder or file by
+	 * this name already exists in the newParent folder
+	 * @throws IOException thrown if an IO or access error occurs.
+	 * @throws CancelledException if task monitor cancelled operation.
+	 */
+	GhidraFolder copyTo(GhidraFolderData newParent, TaskMonitor monitor)
 			throws IOException, CancelledException {
 		synchronized (fileSystem) {
-			if (newParentData.fileSystem.isReadOnly()) {
+			if (newParent.fileSystem.isReadOnly()) {
 				throw new ReadOnlyException("copyTo permitted to writeable project only");
 			}
-			if (isAncestor(newParentData)) {
+			if (isAncestor(newParent)) {
 				throw new IOException("self-referencing copy not permitted");
 			}
-			GhidraFolderData newFolderData = newParentData.getFolderData(name, false);
+			GhidraFolderData newFolderData = newParent.getFolderData(name, false);
 
 			if (newFolderData == null) {
 				try {
-					newFolderData = newParentData.createFolder(name);
+					newFolderData = newParent.createFolder(name);
 				}
 				catch (InvalidNameException e) {
 					throw new AssertException("Unexpected error", e);
@@ -1144,22 +1267,46 @@ class GhidraFolderData {
 		}
 	}
 
-	DomainFile copyToAsLink(GhidraFolderData newParentData) throws IOException {
+	/**
+	 * Create a new link-file in the specified newParent which will reference this folder 
+	 * (i.e., linked-folder). Restrictions:
+	 * <ul>
+	 * <li>Specified newParent must reside within a different project since internal linking is
+	 * not currently supported.</li>
+	 * </ul>
+	 * If this folder is associated with a temporary transient project (i.e., not a locally 
+	 * managed project) the generated link will refer to the remote folder with a remote
+	 * Ghidra URL, otherwise a local project storage path will be used.
+	 * @param newParent new parent folder where link-file is to be created
+	 * @return newly created domain file (i.e., link-file) or null if link use not supported.
+	 * @throws IOException if an IO or access error occurs.
+	 */
+	DomainFile copyToAsLink(GhidraFolderData newParent) throws IOException {
 		synchronized (fileSystem) {
 			String linkFilename = name;
 			if (linkFilename == null) {
-				if (fileManager instanceof TransientProjectData) {
-					linkFilename = fileManager.getRepository().getName();
+				if (projectData instanceof TransientProjectData) {
+					linkFilename = projectData.getRepository().getName();
 				}
 				else {
-					linkFilename = fileManager.getProjectLocator().getName();
+					linkFilename = projectData.getProjectLocator().getName();
 				}
 			}
-			return newParentData.copyAsLink(fileManager, getPathname(), linkFilename,
+			return newParent.copyAsLink(projectData, getPathname(), linkFilename,
 				FolderLinkContentHandler.INSTANCE);
 		}
 	}
 
+	/**
+	 * Create a link-file within this folder.  The link-file may correspond to various types of
+	 * content (e.g., Program, Trace, Folder, etc.) based upon specified link handler.
+	 * @param sourceProjectData referenced content project data within which specified path exists.
+	 * @param pathname path of referenced content with source project data
+	 * @param linkFilename name of link-file to be created within this folder.
+	 * @param lh link file handler used to create specific link file.
+	 * @return link-file 
+	 * @throws IOException if IO error occurs during link creation
+	 */
 	DomainFile copyAsLink(ProjectData sourceProjectData, String pathname, String linkFilename,
 			LinkHandler<?> lh) throws IOException {
 		synchronized (fileSystem) {
@@ -1167,7 +1314,7 @@ class GhidraFolderData {
 				throw new ReadOnlyException("copyAsLink permitted to writeable project only");
 			}
 
-			if (sourceProjectData == fileManager) {
+			if (sourceProjectData == projectData) {
 				// internal linking not yet supported
 				Msg.error(this, "Internal file/folder links not yet supported");
 				return null;
@@ -1177,13 +1324,12 @@ class GhidraFolderData {
 			if (sourceProjectData instanceof TransientProjectData) {
 				RepositoryAdapter repository = sourceProjectData.getRepository();
 				ServerInfo serverInfo = repository.getServerInfo();
-				ghidraUrl =
-					GhidraURL.makeURL(serverInfo.getServerName(), serverInfo.getPortNumber(),
-						repository.getName(), pathname);
+				ghidraUrl = GhidraURL.makeURL(serverInfo.getServerName(),
+					serverInfo.getPortNumber(), repository.getName(), pathname);
 			}
 			else {
 				ProjectLocator projectLocator = sourceProjectData.getProjectLocator();
-				if (projectLocator.equals(fileManager.getProjectLocator())) {
+				if (projectLocator.equals(projectData.getProjectLocator())) {
 					return null; // local internal linking not supported
 				}
 				ghidraUrl = GhidraURL.makeURL(projectLocator, pathname, null);
@@ -1216,6 +1362,14 @@ class GhidraFolderData {
 		}
 	}
 
+	/**
+	 * Generate a non-conflicting file name for this folder based upon the specified preferred name.
+	 * NOTE: This method is subject to race conditions where returned name could conflict by the
+	 * time it is actually used.
+	 * @param preferredName preferred file name
+	 * @return non-conflicting file name
+	 * @throws IOException if an IO error occurs during file checks
+	 */
 	String getTargetName(String preferredName) throws IOException {
 		String newName = preferredName;
 		int i = 1;
@@ -1242,11 +1396,11 @@ class GhidraFolderData {
 
 	@Override
 	public String toString() {
-		ProjectLocator projectLocator = fileManager.getProjectLocator();
+		ProjectLocator projectLocator = projectData.getProjectLocator();
 		if (projectLocator.isTransient()) {
-			return fileManager.getProjectLocator().getName() + getPathname();
+			return projectData.getProjectLocator().getName() + getPathname();
 		}
-		return fileManager.getProjectLocator().getName() + ":" + getPathname();
+		return projectData.getProjectLocator().getName() + ":" + getPathname();
 	}
 
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/RootGhidraFolder.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,8 +19,8 @@ import ghidra.framework.model.DomainFolderChangeListener;
 
 public class RootGhidraFolder extends GhidraFolder {
 
-	RootGhidraFolder(ProjectFileManager fileManager, DomainFolderChangeListener listener) {
-		super(fileManager, listener);
+	RootGhidraFolder(DefaultProjectData projectData, DomainFolderChangeListener listener) {
+		super(projectData, listener);
 	}
 
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/data/RootGhidraFolderData.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -21,18 +20,18 @@ import ghidra.framework.store.FileSystem;
 
 public class RootGhidraFolderData extends GhidraFolderData {
 
-	RootGhidraFolderData(ProjectFileManager fileManager, DomainFolderChangeListener listener) {
-		super(fileManager, listener);
+	RootGhidraFolderData(DefaultProjectData projectData, DomainFolderChangeListener listener) {
+		super(projectData, listener);
 	}
 
 	@Override
 	GhidraFolder getDomainFolder() {
-		return new RootGhidraFolder(getProjectFileManager(), getChangeListener());
+		return new RootGhidraFolder(getProjectData(), getChangeListener());
 	}
 
 	/**
 	 * Provided for testing use only
-	 * @param fs
+	 * @param fs versioned file system
 	 */
 	void setVersionedFileSystem(FileSystem fs) {
 		versionedFileSystem = fs;

Ghidra/Framework/Project/src/main/java/ghidra/framework/model/DomainFile.java

@@ -53,7 +53,7 @@ public interface DomainFile extends Comparable<DomainFile> {
 	public final static String READ_ONLY_PROPERTY = "READ_ONLY";
 
 	/**
-	 * Get the name of  the StoredObj that is associated with the data.
+	 * Get the name of this project file
 	 * @return the name
 	 */
 	public String getName();
@@ -83,7 +83,7 @@ public interface DomainFile extends Comparable<DomainFile> {
 	public DomainFile setName(String newName) throws InvalidNameException, IOException;
 
 	/**
-	 * Returns the path name to the domain object.
+	 * Returns the full path name to this file
 	 * @return the path name
 	 */
 	public String getPathname();
@@ -114,7 +114,7 @@ public interface DomainFile extends Comparable<DomainFile> {
 	public ProjectLocator getProjectLocator();
 
 	/**
-	 * Returns content-type string
+	 * Returns content-type string for this file
 	 * @return the file content type or a reserved content type {@link ContentHandler#MISSING_CONTENT}
 	 * or {@link ContentHandler#UNKNOWN_CONTENT}.
 	 */
@@ -134,8 +134,11 @@ public interface DomainFile extends Comparable<DomainFile> {
 
 	/**
 	 * Returns changes made to versioned file by others since checkout was performed.
+	 * NOTE: This method is unable to cope with version issues which may require an
+	 * upgrade.
 	 * @return change set or null
-	 * @throws VersionException latest version was created with a newer version of software
+	 * @throws VersionException latest version was created with a different version of software
+	 * which prevents rapid determination of change set.
 	 * @throws IOException if a folder item access error occurs or change set was 
 	 * produced by newer version of software and can not be read
 	 */
@@ -426,7 +429,7 @@ public interface DomainFile extends Comparable<DomainFile> {
 	 * @param keep if true, the private database will be renamed with a .keep
 	 * extension.
 	 * @throws NotConnectedException if shared project and not connected to repository
-	 * @throws FileInUseException if this file is in-use / checked-out.
+	 * @throws FileInUseException if this file is in-use.
 	 * @throws IOException if file is not checked-out or an IO / access error occurs.
 	 */
 	public void undoCheckout(boolean keep) throws IOException;
@@ -549,7 +552,8 @@ public interface DomainFile extends Comparable<DomainFile> {
 
 	/**
 	 * Get the list of consumers (Objects) for this domain file.
-	 * @return empty array list if there are no consumers
+	 * @return true if linking is supported allowing a link-file to be created which 
+	 * references this file, else false.
 	 */
 	public List<?> getConsumers();
 
@@ -593,7 +597,7 @@ public interface DomainFile extends Comparable<DomainFile> {
 	/**
 	 * Returns the length of this domain file.  This size is the minimum disk space
 	 * used for storing this file, but does not account for additional storage space
-	 * used to tracks changes, etc. 
+	 * used to track changes, etc. 
 	 * @return file length
 	 * @throws IOException if IO or access error occurs
 	 */

Ghidra/Framework/Project/src/main/java/ghidra/framework/model/DomainFolder.java

@@ -83,7 +83,7 @@ public interface DomainFolder extends Comparable<DomainFolder> {
 	public ProjectData getProjectData();
 
 	/**
-	 * Returns the path name to the domain object.
+	 * Returns the full path name to this folder
 	 * @return the path name
 	 */
 	public String getPathname();
@@ -183,11 +183,10 @@ public interface DomainFolder extends Comparable<DomainFolder> {
 			throws InvalidNameException, IOException, CancelledException;
 
 	/**
-	 * Create a subfolder of this folder.
+	 * Create a subfolder within this folder.
 	 * @param folderName sub-folder name
-	 * @return the folder
-	 * @throws DuplicateFileException if a folder by
-	 * this name already exists
+	 * @return the new folder
+	 * @throws DuplicateFileException if a folder by this name already exists
 	 * @throws InvalidNameException if name is an empty string of if it contains characters other 
 	 * than alphanumerics.
 	 * @throws IOException if IO or access error occurs
@@ -195,16 +194,16 @@ public interface DomainFolder extends Comparable<DomainFolder> {
 	public DomainFolder createFolder(String folderName) throws InvalidNameException, IOException;
 
 	/**
-	 * Deletes this folder and all of its contents
+	 * Deletes this folder, if empty, from the local filesystem
 	 * @throws IOException if IO or access error occurs
-	 * @throws FolderNotEmptyException Thrown if the subfolder is not empty.
+	 * @throws FolderNotEmptyException Thrown if this folder is not empty.
 	 */
 	public void delete() throws IOException;
 
 	/**
-	 * Move this folder into the newParent folder.  If connected to an archive
-	 * this affects both private and repository folders and files.  If not
-	 * connected, only private folders and files are affected.
+	 * Move this folder into the newParent folder.  If connected to a repository
+	 * this moves both private and repository folders/files.  If not
+	 * connected, only private folders/files are moved.
 	 * @param newParent new parent folder within the same project
 	 * @return the newly relocated folder (the original DomainFolder object becomes invalid since 
 	 * it is immutable)
@@ -220,7 +219,7 @@ public interface DomainFolder extends Comparable<DomainFolder> {
 	 * Copy this folder into the newParent folder.
 	 * @param newParent new parent folder
 	 * @param monitor the task monitor
-	 * @return the copied folder
+	 * @return the new copied folder
 	 * @throws DuplicateFileException if a folder or file by
 	 * this name already exists in the newParent folder
 	 * @throws IOException thrown if an IO or access error occurs.
@@ -230,16 +229,17 @@ public interface DomainFolder extends Comparable<DomainFolder> {
 			throws IOException, CancelledException;
 
 	/**
-	 * Copy this folder into the newParent folder as a link file.  Restrictions:
+	 * Create a new link-file in the specified newParent which will reference this folder 
+	 * (i.e., linked-folder). Restrictions:
 	 * <ul>
 	 * <li>Specified newParent must reside within a different project since internal linking is
 	 * not currently supported.</li>
 	 * </ul>
 	 * If this folder is associated with a temporary transient project (i.e., not a locally 
-	 * managed project) the generated link will refer to the remote file with a remote
+	 * managed project) the generated link will refer to the remote folder with a remote
 	 * Ghidra URL, otherwise a local project storage path will be used.
-	 * @param newParent new parent folder
-	 * @return newly created domain file or null if link use not supported.
+	 * @param newParent new parent folder where link-file is to be created
+	 * @return newly created domain file (i.e., link-file) or null if link use not supported.
 	 * @throws IOException if an IO or access error occurs.
 	 */
 	public DomainFile copyToAsLink(DomainFolder newParent) throws IOException;

Ghidra/Framework/Project/src/main/java/ghidra/framework/model/DomainObjectClosedListener.java

@@ -1,6 +1,5 @@
 /* ###
  * IP: GHIDRA
- * REVIEWED: YES
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -20,5 +19,10 @@ package ghidra.framework.model;
  * An interface that allows for a callback when a {@link DomainObject} is closed.
  */
 public interface DomainObjectClosedListener {
-	public void domainObjectClosed();
+
+	/**
+	 * Callback indicating that the specified {@link DomainObject} has been closed.
+	 * @param dobj domain object
+	 */
+	public void domainObjectClosed(DomainObject dobj);
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/model/ProjectData.java

@@ -191,8 +191,10 @@ public interface ProjectData {
 			TaskMonitor monitor) throws IOException, CancelledException;
 
 	/**
-	 * Close the project storage associated with this project data object.
-	 * NOTE: This should not be invoked if this object is utilized by a Project instance.
+	 * Initiate disposal of this project data object.  Any files already open will delay 
+	 * disposal until they are closed.
+	 * NOTE: This should only be invoked by the controlling object which created/opened this
+	 * instance to avoid premature disposal. 
 	 */
 	public void close();
 
@@ -209,4 +211,18 @@ public interface ProjectData {
 	 */
 	public void testValidName(String name, boolean isPath) throws InvalidNameException;
 
+	/**
+	 * Generate a repository URL which corresponds to this project data if applicable.
+	 * Local private projects will return null;
+	 * @return repository URL which corresponds to this project data or null if not applicable.
+	 */
+	public URL getSharedProjectURL();
+
+	/**
+	 * Generate a local URL which corresponds to this project data if applicable.
+	 * Remote transient project data will return null;
+	 * @return local URL which corresponds to this project data or null if not applicable.
+	 */
+	public URL getLocalProjectURL();
+
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/project/DefaultProject.java

@@ -25,7 +25,7 @@ import org.jdom.input.SAXBuilder;
 import org.jdom.output.XMLOutputter;
 
 import ghidra.framework.client.RepositoryAdapter;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.data.TransientDataManager;
 import ghidra.framework.model.*;
 import ghidra.framework.options.SaveState;
@@ -58,7 +58,7 @@ public class DefaultProject implements Project {
 	private DefaultProjectManager projectManager;
 
 	private ProjectLocator projectLocator;
-	private ProjectFileManager fileMgr;
+	private DefaultProjectData projectData;
 	private ToolManagerImpl toolManager;
 
 	private boolean changed; // flag for whether the project configuration has changed
@@ -66,7 +66,7 @@ public class DefaultProject implements Project {
 
 	private Map<String, SaveState> dataMap = new HashMap<>();
 	private Map<String, ToolTemplate> projectConfigMap = new HashMap<>();
-	private Map<URL, ProjectFileManager> otherViews = new HashMap<>();
+	private Map<URL, DefaultProjectData> otherViewsMap = new HashMap<>();
 	private Set<URL> visibleViews = new HashSet<>();
 	private WeakSet<ProjectViewListener> viewListeners =
 		WeakDataStructureFactory.createCopyOnWriteWeakSet();
@@ -86,22 +86,11 @@ public class DefaultProject implements Project {
 		this.projectManager = projectManager;
 		this.projectLocator = projectLocator;
 
-		boolean success = false;
-		try {
 		Msg.info(this, "Creating project: " + projectLocator.toString());
-			fileMgr = new ProjectFileManager(projectLocator, repository, true);
+		projectData = new DefaultProjectData(projectLocator, repository, true);
 		if (!SystemUtilities.isInHeadlessMode()) {
 			toolManager = new ToolManagerImpl(this);
 		}
-			success = true;
-		}
-		finally {
-			if (!success) {
-				if (fileMgr != null) {
-					fileMgr.dispose();
-				}
-			}
-		}
 		initializeNewProject();
 	}
 
@@ -122,28 +111,18 @@ public class DefaultProject implements Project {
 		this.projectManager = projectManager;
 		this.projectLocator = projectLocator;
 
-		boolean success = false;
-		try {
 		Msg.info(this, "Opening project: " + projectLocator.toString());
-			fileMgr = new ProjectFileManager(projectLocator, true, resetOwner);
+		projectData = new DefaultProjectData(projectLocator, true, resetOwner);
 		if (!SystemUtilities.isInHeadlessMode()) {
 			toolManager = new ToolManagerImpl(this);
 		}
-			success = true;
-		}
-		finally {
-			if (!success) {
-				if (fileMgr != null) {
-					fileMgr.dispose();
-				}
-			}
-		}
 	}
 
 	/**
 	 * Constructor for opening a URL-based project
 	 * 
-	 * @param connection project connection
+	 * @param projectManager the manager of this project
+	 * @param connection project URL connection (not previously used)
 	 * @throws IOException if I/O error occurs.
 	 */
 	protected DefaultProject(DefaultProjectManager projectManager, GhidraURLConnection connection)
@@ -151,27 +130,17 @@ public class DefaultProject implements Project {
 
 		this.projectManager = projectManager;
 
-		boolean success = false;
-		try {
 		Msg.info(this, "Opening project/repository: " + connection.getURL());
-			fileMgr = (ProjectFileManager) connection.getProjectData();
-			if (fileMgr == null) {
+		projectData = (DefaultProjectData) connection.getProjectData();
+		if (projectData == null) {
 			throw new IOException("Failed to open project/repository: " + connection.getURL());
 		}
 
-			projectLocator = fileMgr.getProjectLocator();
+		projectLocator = projectData.getProjectLocator();
 		if (!SystemUtilities.isInHeadlessMode()) {
 			toolManager = new ToolManagerImpl(this);
 		}
-			success = true;
-		}
-		finally {
-			if (!success) {
-				if (fileMgr != null) {
-					fileMgr.dispose();
-				}
-			}
-		}
+
 		initializeNewProject();
 	}
 
@@ -300,20 +269,20 @@ public class DefaultProject implements Project {
 			return null;
 		}
 
-		ProjectFileManager projectData = (ProjectFileManager) c.getProjectData();
+		DefaultProjectData projectData = (DefaultProjectData) c.getProjectData();
 		if (projectData == null) {
 			throw new IOException(
 				"Failed to view specified project/repository: " + GhidraURL.getDisplayString(url));
 		}
 		url = projectData.getProjectLocator().getURL(); // transform to repository root URL
 
-		otherViews.put(url, projectData);
+		otherViewsMap.put(url, projectData);
 		return projectData;
 	}
 
 	@Override
 	public ProjectData addProjectView(URL url, boolean visible) throws IOException {
-		synchronized (otherViews) {
+		synchronized (otherViewsMap) {
 			if (isClosed) {
 				throw new IOException("project is closed");
 			}
@@ -322,7 +291,7 @@ public class DefaultProject implements Project {
 				throw new IOException("Invalid Ghidra URL specified: " + url);
 			}
 
-			ProjectData projectData = otherViews.get(url);
+			ProjectData projectData = otherViewsMap.get(url);
 			if (projectData == null) {
 				projectData = openProjectView(url);
 			}
@@ -340,13 +309,13 @@ public class DefaultProject implements Project {
 	 */
 	@Override
 	public void removeProjectView(URL url) {
-		synchronized (otherViews) {
-			ProjectFileManager dataMgr = otherViews.remove(url);
+		synchronized (otherViewsMap) {
+			DefaultProjectData dataMgr = otherViewsMap.remove(url);
 			if (dataMgr != null) {
 				if (visibleViews.remove(url)) {
 					notifyVisibleViewRemoved(url);
 				}
-				dataMgr.dispose();
+				dataMgr.close();
 				Msg.info(this, "Closed project view: " + GhidraURL.getDisplayString(url));
 				changed = true;
 			}
@@ -401,22 +370,20 @@ public class DefaultProject implements Project {
 
 	@Override
 	public RepositoryAdapter getRepository() {
-		return fileMgr.getRepository();
+		return projectData.getRepository();
 	}
 
 	@Override
 	public void close() {
-		synchronized (otherViews) {
+		synchronized (otherViewsMap) {
 			isClosed = true;
 
-			Iterator<ProjectFileManager> iter = otherViews.values().iterator();
-			while (iter.hasNext()) {
-				ProjectFileManager dataMgr = iter.next();
+			for (DefaultProjectData dataMgr : otherViewsMap.values()) {
 				if (dataMgr != null) {
-					dataMgr.dispose();
+					dataMgr.close();
 				}
 			}
-			otherViews.clear();
+			otherViewsMap.clear();
 		}
 
 		try {
@@ -429,7 +396,7 @@ public class DefaultProject implements Project {
 			}
 		}
 		finally {
-			fileMgr.dispose();
+			projectData.close();
 		}
 	}
 
@@ -449,7 +416,7 @@ public class DefaultProject implements Project {
 	@Override
 	public void restore() {
 		// if there is a saved project, restore it
-		File saveFile = new File(fileMgr.getProjectDir(), PROJECT_STATE);
+		File saveFile = new File(projectData.getProjectDir(), PROJECT_STATE);
 		String errorMsg = null;
 		Throwable error = null;
 		try {
@@ -593,7 +560,7 @@ public class DefaultProject implements Project {
 		try {
 			// save tool state
 			root.addContent(toolManager.saveToXml()); // the tool manager will save the open tools' state
-			File saveFile = new File(fileMgr.getProjectDir(), PROJECT_STATE);
+			File saveFile = new File(projectData.getProjectDir(), PROJECT_STATE);
 			OutputStream os = new FileOutputStream(saveFile);
 			Document doc = new Document(root);
 			XMLOutputter xmlOut = new GenericXMLOutputter();
@@ -629,15 +596,14 @@ public class DefaultProject implements Project {
 	@Override
 	public List<DomainFile> getOpenData() {
 		ArrayList<DomainFile> openFiles = new ArrayList<>();
-		fileMgr.findOpenFiles(openFiles);
+		projectData.findOpenFiles(openFiles);
 		ProjectData[] viewedProjs = getViewedProjectData();
 		for (ProjectData viewedProj : viewedProjs) {
-			((ProjectFileManager) viewedProj).findOpenFiles(openFiles);
+			((DefaultProjectData) viewedProj).findOpenFiles(openFiles);
 		}
 		List<DomainFile> list = new ArrayList<>();
 		TransientDataManager.getTransients(list);
-		for (int i = 0; i < list.size(); i++) {
-			DomainFile df = list.get(i);
+		for (DomainFile df : list) {
 			if (df != null && df.isOpen()) {
 				openFiles.add(df);
 			}
@@ -646,8 +612,8 @@ public class DefaultProject implements Project {
 	}
 
 	@Override
-	public ProjectFileManager getProjectData() {
-		return fileMgr;
+	public DefaultProjectData getProjectData() {
+		return projectData;
 	}
 
 	@Override
@@ -662,12 +628,12 @@ public class DefaultProject implements Project {
 
 	@Override
 	public ProjectData getProjectData(ProjectLocator locator) {
-		if (locator.equals(fileMgr.getProjectLocator())) {
-			return fileMgr;
+		if (locator.equals(projectData.getProjectLocator())) {
+			return projectData;
 		}
 
-		synchronized (otherViews) {
-			for (ProjectData data : otherViews.values()) {
+		synchronized (otherViewsMap) {
+			for (ProjectData data : otherViewsMap.values()) {
 				if (locator.equals(data.getProjectLocator())) {
 					return data;
 				}
@@ -680,30 +646,30 @@ public class DefaultProject implements Project {
 	@Override
 	public ProjectData getProjectData(URL url) {
 		if (projectLocator.getURL().equals(url)) {
-			return fileMgr;
+			return projectData;
 		}
 		URL remoteURL = getProjectData().getRootFolder().getSharedProjectURL();
 		if (remoteURL != null) {
 			remoteURL = GhidraURL.getProjectURL(url);
 		}
 		if (remoteURL.equals(url)) {
-			return fileMgr;
+			return projectData;
 		}
 
-		synchronized (otherViews) {
-			return otherViews.get(url);
+		synchronized (otherViewsMap) {
+			return otherViewsMap.get(url);
 		}
 	}
 
 	@Override
 	public ProjectData[] getViewedProjectData() {
-		synchronized (otherViews) {
+		synchronized (otherViewsMap) {
 
 			// only return visible viewed project
 			List<ProjectData> list = new ArrayList<>();
-			for (URL url : otherViews.keySet()) {
+			for (URL url : otherViewsMap.keySet()) {
 				if (visibleViews.contains(url)) {
-					list.add(otherViews.get(url));
+					list.add(otherViewsMap.get(url));
 				}
 			}
 
@@ -715,11 +681,9 @@ public class DefaultProject implements Project {
 
 	@Override
 	public void releaseFiles(Object consumer) {
-		fileMgr.releaseDomainFiles(consumer);
-		synchronized (otherViews) {
-			Iterator<ProjectFileManager> it = otherViews.values().iterator();
-			while (it.hasNext()) {
-				ProjectFileManager mgr = it.next();
+		projectData.releaseDomainFiles(consumer);
+		synchronized (otherViewsMap) {
+			for (DefaultProjectData mgr : otherViewsMap.values()) {
 				mgr.releaseDomainFiles(consumer);
 			}
 		}

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/DefaultGhidraProtocolConnector.java

@@ -78,6 +78,7 @@ public class DefaultGhidraProtocolConnector extends GhidraProtocolConnector {
 			}
 			catch (RepositoryNotFoundException e) {
 				statusCode = StatusCode.NOT_FOUND;
+				return statusCode;
 			}
 		}
 		else if (!repositoryServerAdapter.isCancelled()) {

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/DefaultLocalGhidraProtocolConnector.java

@@ -21,7 +21,7 @@ import java.net.URL;
 
 import ghidra.framework.client.NotConnectedException;
 import ghidra.framework.client.RepositoryAdapter;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.ProjectLocator;
 import ghidra.framework.protocol.ghidra.GhidraURLConnection.StatusCode;
 import ghidra.framework.store.LockException;
@@ -126,13 +126,13 @@ public class DefaultLocalGhidraProtocolConnector extends GhidraProtocolConnector
 	 * @return project data instance or null if project not found
 	 * @throws IOException if IO error occurs
 	 */
-	ProjectFileManager getLocalProjectData(boolean readOnlyAccess) throws IOException {
+	DefaultProjectData getLocalProjectData(boolean readOnlyAccess) throws IOException {
 		if (connect(readOnlyAccess) != StatusCode.OK) {
 			return null;
 		}
 
 		try {
-			return new ProjectFileManager(localStorageLocator, !readOnlyAccess, false);
+			return new DefaultProjectData(localStorageLocator, !readOnlyAccess, false);
 		}
 		catch (NotOwnerException | ReadOnlyException e) {
 			statusCode = StatusCode.UNAUTHORIZED;

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/GhidraURLConnection.java

@@ -19,7 +19,7 @@ import java.io.*;
 import java.net.*;
 
 import ghidra.framework.client.*;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.ProjectData;
 import ghidra.util.exception.AssertException;
 
@@ -69,38 +69,6 @@ public class GhidraURLConnection extends URLConnection {
 		}
 	}
 
-	// TODO: consider implementing request and response headers
-
-//	/**
-//	 * Ghidra Status-Code 200: OK.
-//	 */
-//	public static final int GHIDRA_OK = 200;
-//
-//	/**
-//	 * Ghidra Status-Code 401: Unauthorized.
-//	 * This response code includes a variety of connection errors
-//	 * which are reported/logged by the Ghidra Server support code.
-//	 */
-//	public static final int GHIDRA_UNAUTHORIZED = 401;
-//
-//	/**
-//	 * Ghidra Status-Code 404: Not Found.
-//	 */
-//	public static final int GHIDRA_NOT_FOUND = 404;
-//
-//	/**
-//	 * Ghidra Status-Code 423: Locked
-//	 * Caused by attempt to open local project data with write-access when project is
-//	 * already opened and locked.
-//	 */
-//	public static final int GHIDRA_LOCKED = 423;
-//
-//	/**
-//	 * Ghidra Status-Code 503: Unavailable
-//	 * Caused by other connection failure
-//	 */
-//	public static final int GHIDRA_UNAVAILABLE = 503;
-
 	/**
 	 * Ghidra content type - domain folder/file wrapped within GhidraURLWrappedContent object.
 	 * @see GhidraURLWrappedContent
@@ -117,7 +85,7 @@ public class GhidraURLConnection extends URLConnection {
 
 	private GhidraProtocolConnector protocolConnector;
 
-	private ProjectFileManager projectData;
+	private DefaultProjectData projectData;
 	private Object refObject;
 
 	private boolean readOnly = true;
@@ -270,12 +238,17 @@ public class GhidraURLConnection extends URLConnection {
 	}
 
 	/**
-	 * If URL connects and corresponds to a valid repository, this method
+	 * If URL connects and corresponds to a valid repository or local project, this method
 	 * may be used to obtain the associated ProjectData object.  The caller is
-	 * responsible for closing the returned project data when no longer in-use,
-	 * failure to do so may prevent release of repository handle to server.
-	 * Only a single call to this method is permitted.
-	 * @return transient project data or null if unavailable
+	 * responsible for properly {@link ProjectData#close() closing} the returned project data 
+	 * instance when no longer in-use, failure to do so may prevent release of repository handle 
+	 * to server until process exits.  It is important that {@link ProjectData#close()} is
+	 * invoked once, and only once, per call to this method to ensure project "use" tracking 
+	 * is properly maintained.  Improperly invoking the close method on a shared transient 
+	 * {@link ProjectData} instance may cause the underlying storage to be prematurely
+	 * disposed. 
+	 * 
+	 * @return project data which corresponds to this connection or null if unavailable
 	 * @throws IOException if an IO error occurs
 	 */
 	public ProjectData getProjectData() throws IOException {

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/GhidraURLWrappedContent.java

@@ -20,6 +20,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.List;
 
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.*;
 import ghidra.util.InvalidNameException;
 
@@ -43,7 +44,7 @@ public class GhidraURLWrappedContent {
 
 	private List<Object> consumers = new ArrayList<Object>();
 
-	private ProjectData projectData;
+	private DefaultProjectData projectData;
 	private Object refObject;
 
 	public GhidraURLWrappedContent(GhidraURLConnection c) {
@@ -82,6 +83,8 @@ public class GhidraURLWrappedContent {
 
 	/**
 	 * Close associated {@link ProjectData} when all consumers have released wrapped object.
+	 * Underlying project data instance may remain active until all open project files have been
+	 * released/closed.
 	 */
 	private void closeProjectData() {
 		if (projectData != null) {
@@ -91,8 +94,8 @@ public class GhidraURLWrappedContent {
 		refObject = null;
 	}
 
-	private DomainFolder getExplicitFolder(String folderPath) throws InvalidNameException,
-			IOException {
+	private DomainFolder getExplicitFolder(String folderPath)
+			throws InvalidNameException, IOException {
 		DomainFolder folder = projectData.getRootFolder();
 		for (String name : folderPath.substring(1).split("/")) {
 			DomainFolder subfolder = folder.getFolder(name);
@@ -110,7 +113,7 @@ public class GhidraURLWrappedContent {
 			return;
 		}
 
-		projectData = c.getProjectData();
+		projectData = (DefaultProjectData) c.getProjectData();
 
 		String folderItemName = c.getFolderItemName();
 		String folderPath = c.getFolderPath();

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/TransientProjectData.java

@@ -16,10 +16,11 @@
 package ghidra.framework.protocol.ghidra;
 
 import java.io.IOException;
+import java.net.URL;
 
 import generic.timer.GhidraSwinglessTimer;
 import ghidra.framework.client.RepositoryAdapter;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.ProjectLocator;
 import ghidra.framework.remote.RepositoryHandle;
 import ghidra.framework.store.LockException;
@@ -27,7 +28,7 @@ import ghidra.util.Msg;
 import ghidra.util.SystemUtilities;
 import utilities.util.FileUtilities;
 
-public class TransientProjectData extends ProjectFileManager {
+public class TransientProjectData extends DefaultProjectData {
 
 	private TransientProjectManager dataMgr;
 	final RepositoryInfo repositoryInfo;
@@ -146,23 +147,30 @@ public class TransientProjectData extends ProjectFileManager {
 			}
 			stopCleanupTimer();
 			disposed = true;
-		}
 
-		Msg.debug(this, "Removing transient project (" + repositoryInfo.toShortString() + "): " +
-			getProjectLocator().getProjectDir());
+			String msgTail = " transient project (" + repositoryInfo.toShortString() + "): " +
+				getProjectLocator().getProjectDir() + ", URL: " + repositoryInfo.getURL();
+			if (instanceUseCount != 0) {
+				Msg.error(this, "Premature removal of active" + msgTail);
+			}
+			else {
+				Msg.debug(this, "Removing idle" + msgTail);
+			}
+		}
 
 		dataMgr.cleanupProjectData(repositoryInfo, this);
 
 		super.dispose(); // disconnects repository
 
-		// TODO: There could still be open files if they have not been properly released/closed !!
+		// Remove temporary project storage
+		// NOTE: This could be affected by project files which still remain open
 		ProjectLocator locator = getProjectLocator();
 		FileUtilities.deleteDir(locator.getProjectDir());
 		locator.getMarkerFile().delete();
 	}
 
 	@Override
-	public void dispose() {
+	public void close() {
 		// prevent normal disposal - rely on finalizer and shutdown hook
 		synchronized (cleanupTimer) {
 			if (instanceUseCount == 0) {
@@ -178,13 +186,18 @@ public class TransientProjectData extends ProjectFileManager {
 	}
 
 	@Override
-	protected void finalize() throws Throwable {
-		try {
-			forcedDispose();
+	protected void dispose() {
+		// rely on forcedDispose to invoke super.dispose()
 	}
-		catch (Throwable t) {
-			// ignore errors during finalize
+
+	@Override
+	public URL getSharedProjectURL() {
+		return repositoryInfo.getURL();
 	}
-		super.finalize();
+
+	@Override
+	public URL getLocalProjectURL() {
+		return null;
 	}
+
 }

Ghidra/Framework/Project/src/main/java/ghidra/framework/protocol/ghidra/TransientProjectManager.java

@@ -71,8 +71,9 @@ public class TransientProjectManager {
 	}
 
 	private TransientProjectManager() {
-		Runtime.getRuntime().addShutdownHook(
-			new Thread((Runnable) () -> dispose(), "TransientProjectManager Shutdown Hook"));
+		Runtime.getRuntime()
+				.addShutdownHook(new Thread((Runnable) () -> dispose(),
+					"TransientProjectManager Shutdown Hook"));
 	}
 
 	/**
@@ -80,8 +81,6 @@ public class TransientProjectManager {
 	 * connections. WARNING: This method intended for testing only.
 	 */
 	public synchronized void dispose() {
-		// TODO: server handles may be shared with non-transient projects
-
 		TransientProjectData[] projectDataArray =
 			repositoryMap.values().toArray(new TransientProjectData[repositoryMap.size()]);
 		for (TransientProjectData projectData : projectDataArray) {

Ghidra/Framework/Project/src/main/java/ghidra/framework/task/GTaskManager.java

@@ -15,17 +15,16 @@
  */
 package ghidra.framework.task;
 
-import generic.concurrent.GThreadPool;
-import ghidra.framework.model.DomainObjectClosedListener;
-import ghidra.framework.model.UndoableDomainObject;
-import ghidra.util.Msg;
-import ghidra.util.exception.CancelledException;
-
 import java.util.*;
 import java.util.concurrent.TimeUnit;
 import java.util.concurrent.locks.Condition;
 import java.util.concurrent.locks.ReentrantLock;
 
+import generic.concurrent.GThreadPool;
+import ghidra.framework.model.*;
+import ghidra.util.Msg;
+import ghidra.util.exception.CancelledException;
+
 /** 
  * Class for managing a queue of tasks to be executed, one at a time, in priority order.  All the
  * tasks pertain to an UndoableDomainObject and transactions are created on the UndoableDomainObject
@@ -95,7 +94,8 @@ public class GTaskManager {
 
 		domainObject.addCloseListener(new DomainObjectClosedListener() {
 			@Override
-			public void domainObjectClosed() {
+			public void domainObjectClosed(DomainObject dobj) {
+				// assert dobj == domainObj
 				GTaskManagerFactory.domainObjectClosed(domainObject);
 				domainObject = null;
 			}
@@ -107,7 +107,7 @@ public class GTaskManager {
 	 * 
 	 * @param task the task to be run.
 	 * @param priority the priority of the task.  Lower numbers are run before higher numbers.
-	 * @param useCurrentGroup. If true, this task will be rolled into the current transaction group
+	 * @param useCurrentGroup If true, this task will be rolled into the current transaction group
 	 * 							if one exists.  If false, any open transaction 
 	 * 							will be closed and a new transaction will be opened before 
 	 * 							this task is run.
@@ -680,7 +680,8 @@ public class GTaskManager {
 			taskListener.taskCompleted(task, result);
 		}
 		catch (Throwable unexpected) {
-			Msg.error(this, "Unexpected exception notifying listener of task completed", unexpected);
+			Msg.error(this, "Unexpected exception notifying listener of task completed",
+				unexpected);
 		}
 	}
 
@@ -705,7 +706,8 @@ public class GTaskManager {
 			taskListener.taskScheduled(scheduledTask);
 		}
 		catch (Throwable unexpected) {
-			Msg.error(this, "Unexpected exception notifying listener of task scheduled", unexpected);
+			Msg.error(this, "Unexpected exception notifying listener of task scheduled",
+				unexpected);
 		}
 	}
 

Ghidra/Framework/Project/src/test/java/ghidra/framework/model/TestDummyProjectData.java

@@ -16,6 +16,7 @@
 package ghidra.framework.model;
 
 import java.io.IOException;
+import java.net.URL;
 import java.util.List;
 
 import ghidra.framework.client.RepositoryAdapter;
@@ -95,6 +96,18 @@ public class TestDummyProjectData implements ProjectData {
 		return null;
 	}
 
+	@Override
+	public URL getSharedProjectURL() {
+		// stub
+		return null;
+	}
+
+	@Override
+	public URL getLocalProjectURL() {
+		// stub
+		return null;
+	}
+
 	@Override
 	public void addDomainFolderChangeListener(DomainFolderChangeListener listener) {
 		// stub

Ghidra/Test/IntegrationTest/src/screen/java/help/screenshot/FrontEndPluginScreenShots.java

@@ -36,7 +36,7 @@ import docking.wizard.WizardPanel;
 import generic.theme.GThemeDefaults.Colors;
 import ghidra.app.plugin.core.archive.RestoreDialog;
 import ghidra.framework.data.GhidraFileData;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.main.*;
 import ghidra.framework.model.*;
 import ghidra.framework.plugintool.dialog.*;
@@ -694,7 +694,7 @@ public class FrontEndPluginScreenShots extends GhidraScreenShotGenerator {
 
 		Project project = env.getProject();
 		program = env.getProgram("WinHelloCPP.exe");
-		ProjectFileManager projectData = (ProjectFileManager) project.getProjectData();
+		DefaultProjectData projectData = (DefaultProjectData) project.getProjectData();
 		projectData.getRootFolder().createFile("HelloCpp.exe", program, TaskMonitor.DUMMY);
 
 		// Create other project to be viewed

Ghidra/Test/IntegrationTest/src/test.slow/java/ghidra/framework/main/ProjectInfoFilesystemTest.java

@@ -26,7 +26,7 @@ import org.junit.*;
 
 import docking.action.DockingActionIf;
 import generic.test.TestUtils;
-import ghidra.framework.data.ProjectFileManager;
+import ghidra.framework.data.DefaultProjectData;
 import ghidra.framework.model.*;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.framework.store.ItemCheckoutStatus;
@@ -276,7 +276,7 @@ public class ProjectInfoFilesystemTest extends AbstractGhidraHeadedIntegrationTe
 	}
 
 	private void checkProjectInfo(Class<?> filesystemClass, String storageType) {
-		ProjectFileManager projectData = (ProjectFileManager) project.getProjectData();
+		DefaultProjectData projectData = (DefaultProjectData) project.getProjectData();
 		String msg = "Expected " + filesystemClass.getSimpleName() + ": ";
 		assertTrue(msg + "Local FileSystem", filesystemClass.isInstance(
 			TestUtils.invokeInstanceMethod("getLocalFileSystem", projectData)));

Ghidra/Test/IntegrationTest/src/test.slow/java/ghidra/server/remote/ServerTestUtil.java

@@ -802,9 +802,9 @@ public class ServerTestUtil {
 	public static void createRepositoryItem(LocalFileSystem repoFilesystem, String name,
 			String folderPath, Program program) throws Exception {
 
-		ContentHandler contentHandler = DomainObjectAdapter.getContentHandler(program);
-		long checkoutId = contentHandler.createFile(repoFilesystem, null, folderPath, name,
-			program, TaskMonitor.DUMMY);
+		ContentHandler<?> contentHandler = DomainObjectAdapter.getContentHandler(program);
+		long checkoutId = contentHandler.createFile(repoFilesystem, null, folderPath, name, program,
+			TaskMonitor.DUMMY);
 		LocalFolderItem item = repoFilesystem.getItem(folderPath, name);
 		if (item == null) {
 			throw new IOException("Item not found: " + FileSystem.SEPARATOR + name);