Merge remote-tracking branch 'origin/Ghidra_9.2'

Ghidra/Features/Base/src/main/java/ghidra/app/nav/Navigatable.java

@@ -35,6 +35,7 @@ public interface Navigatable {
 
 	/**
 	 * Commands this navigatable to goto (display) the given program and location
+	 * @param program the program
 	 * 
 	 * @param location the location in that program to display
 	 * @return true if the goto was successful

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/disassembler/AddressTable.java

@@ -217,7 +217,7 @@ public class AddressTable {
 	 * @param end end index (inclusive)
 	 * @param createIndex don't create index if false
 	 * @param autoLabel true if labels should be created on the table
-	 * @return
+	 * @return true if tablecreated else false
 	 */
 	public boolean makeTable(Program program, int start, int end, boolean createIndex,
 			boolean autoLabel) {
@@ -236,13 +236,17 @@ public class AddressTable {
 
 		//TODO: Do I need to do something special for the 3 byte pointers or will it know
 		// how to make it automatically?
+		DataTypeManager dtm = program.getDataTypeManager();
 		if (shiftedAddr) {
 			adt = ShiftedAddressDataType.dataType;
 		}
-		else {
+		else if (addrSize == program.getDefaultPointerSize()) {
-			adt = new PointerDataType(DataType.DEFAULT, addrSize);
+			adt = new PointerDataType(DataType.DEFAULT, dtm);
 		}
-		adt = program.getDataTypeManager().resolve(adt, null);
+		else {
+			adt = new PointerDataType(DataType.DEFAULT, addrSize, dtm);
+		}
+		adt = dtm.resolve(adt, null);
 
 		Address newAddress = currentAddress;
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/osgi/BundleHost.java

@@ -691,15 +691,9 @@ public class BundleHost {
 	public void activateAll(Collection<GhidraBundle> bundles, TaskMonitor monitor,
 			PrintWriter console) {
 
-		List<GhidraBundle> availableBundles = getGhidraBundles().stream()
+		BundleDependencyGraph dependencyGraph = new BundleDependencyGraph(bundles, monitor);
-				.filter(GhidraBundle::isEnabled)
-				.collect(Collectors.toList());
-
-		BundleDependencyGraph dependencyGraph =
-			new BundleDependencyGraph(availableBundles, bundles, monitor);
 
 		monitor.setMaximum(dependencyGraph.vertexSet().size());
-
 		for (GhidraBundle bundle : dependencyGraph.inTopologicalOrder()) {
 			if (monitor.isCancelled()) {
 				break;
@@ -728,21 +722,25 @@ public class BundleHost {
 	 */
 	public void activateInStages(Collection<GhidraBundle> bundles, TaskMonitor monitor,
 			PrintWriter console) {
-		List<GhidraBundle> bundlesRemaining = new ArrayList<>(bundles);
+		Map<GhidraBundle, List<BundleRequirement>> requirementMap = new HashMap<>();
+		for (GhidraBundle bundle : bundles) {
+			try {
+				requirementMap.put(bundle, bundle.getAllRequirements());
+			}
+			catch (GhidraBundleException e) {
+				fireBundleException(e);
+			}
+		}
+		List<GhidraBundle> bundlesRemaining = new ArrayList<>(requirementMap.keySet());
 
 		monitor.setMaximum(bundlesRemaining.size());
 		while (!bundlesRemaining.isEmpty() && !monitor.isCancelled()) {
-			List<GhidraBundle> resolvableBundles = bundlesRemaining.stream().filter(bundle -> {
+			List<GhidraBundle> resolvableBundles = bundlesRemaining.stream()
-				try {
+					.filter(bundle -> canResolveAll(requirementMap.get(bundle)))
-					return canResolveAll(bundle.getAllRequirements());
+					.collect(Collectors.toList());
-				}
-				catch (GhidraBundleException e) {
-					// failure in last round will set fireBundleException
-				}
-				return false;
-			}).collect(Collectors.toList());
 			if (resolvableBundles.isEmpty()) {
-				// final round, try everything we couldn't resolve to generate errors
+				// final round, try everything that hasn't already been eliminated.
+				// this can generate helpful error messages
 				resolvableBundles = bundlesRemaining;
 				bundlesRemaining = Collections.emptyList();
 			}
@@ -927,18 +925,29 @@ public class BundleHost {
 		// exists only to be distinguished by id
 	}
 
-	private static class BundleDependencyGraph
+	/**
-			extends DirectedMultigraph<GhidraBundle, Dependency> {
+	 *	Utility class to build a dependency graph from bundles where capabilities map to requirements.
+	 */
+	private class BundleDependencyGraph extends DirectedMultigraph<GhidraBundle, Dependency> {
 		final Map<GhidraBundle, List<BundleCapability>> capabilityMap = new HashMap<>();
 		final List<GhidraBundle> availableBundles;
 		final TaskMonitor monitor;
 
-		BundleDependencyGraph(List<GhidraBundle> availableBundles,
+		BundleDependencyGraph(Collection<GhidraBundle> startingBundles, TaskMonitor monitor) {
-				Collection<GhidraBundle> startingBundles, TaskMonitor monitor) {
 			super(null, null, false);
-			this.availableBundles = availableBundles;
 			this.monitor = monitor;
 
+			// maintain a list of bundles available for resolution, starting with all of the enabled bundles
+			this.availableBundles = new ArrayList<>();
+			for (GhidraBundle bundle : getGhidraBundles()) {
+				if (bundle.isEnabled()) {
+					addToAvailable(bundle);
+				}
+			}
+			// An edge A->B indicates that the capabilities of A resolve some requirement(s) of B
+
+			// "front" accumulates bundles and links to bundles already in the graph that they provide capabilities for.
+			//   e.g.  if front[A]=[B,...] then A->B, B is already in the graph, and we will add A next iteration. 
 			Map<GhidraBundle, Set<GhidraBundle>> front = new HashMap<>();
 			for (GhidraBundle bundle : startingBundles) {
 				front.put(bundle, null);
@@ -951,6 +960,7 @@ public class BundleHost {
 				for (GhidraBundle bundle : front.keySet()) {
 					resolve(bundle, newFront);
 				}
+
 				handleBackEdges(newFront);
 				front = newFront;
 			}
@@ -969,8 +979,10 @@ public class BundleHost {
 				GhidraBundle source = entry.getKey();
 				if (containsVertex(source)) {
 					for (GhidraBundle destination : entry.getValue()) {
+						if (source != destination) {
 							addEdge(source, destination, new Dependency());
 						}
+					}
 					newFrontIter.remove();
 				}
 			}
@@ -979,7 +991,7 @@ public class BundleHost {
 		void addFront(Map<GhidraBundle, Set<GhidraBundle>> front) {
 			for (Entry<GhidraBundle, Set<GhidraBundle>> e : front.entrySet()) {
 				GhidraBundle source = e.getKey();
-				availableBundles.add(source);
+				if (addToAvailable(source)) {
 					addVertex(source);
 					Set<GhidraBundle> destinations = e.getValue();
 					if (destinations != null) {
@@ -989,21 +1001,38 @@ public class BundleHost {
 					}
 				}
 			}
+		}
 
+		boolean addToAvailable(GhidraBundle bundle) {
+			try {
+				capabilityMap.put(bundle, bundle.getAllCapabilities());
+				availableBundles.add(bundle);
+				return true;
+			}
+			catch (GhidraBundleException ex) {
+				fireBundleException(ex);
+				return false;
+			}
+		}
+
+		// populate newFront with edges depBundle -> bundle,
+		// where depBundle has a capability that resolves a requirement of bundle
 		void resolve(GhidraBundle bundle, Map<GhidraBundle, Set<GhidraBundle>> newFront) {
 			List<BundleRequirement> requirements;
 			try {
 				requirements = new ArrayList<>(bundle.getAllRequirements());
+				if (requirements.isEmpty()) {
+					return;
+				}
 			}
 			catch (GhidraBundleException e) {
-				throw new RuntimeException(e);
+				fireBundleException(e);
-			}
+				removeVertex(bundle);
-			if (requirements.isEmpty()) {
 				return;
 			}
 
 			for (GhidraBundle depBundle : availableBundles) {
-				for (BundleCapability capability : getCapabilities(depBundle)) {
+				for (BundleCapability capability : capabilityMap.get(depBundle)) {
 					if (monitor.isCancelled()) {
 						return;
 					}
@@ -1020,18 +1049,8 @@ public class BundleHost {
 					}
 				}
 			}
-		}
+			// if requirements remain, some will be resolved by system 
-
+			//  and others will generate helpful errors for the user during activation
-		List<BundleCapability> getCapabilities(GhidraBundle bundle) {
-			return capabilityMap.computeIfAbsent(bundle, b -> {
-				try {
-					return b.getAllCapabilities();
-				}
-				catch (GhidraBundleException e) {
-					Msg.error(this, "getting capabilities", e);
-					return null;
-				}
-			});
 		}
 	}
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/osgi/BundleStatusComponentProvider.java

@@ -36,8 +36,7 @@ import ghidra.app.services.ConsoleService;
 import ghidra.framework.plugintool.ComponentProviderAdapter;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.framework.preferences.Preferences;
-import ghidra.util.HelpLocation;
+import ghidra.util.*;
-import ghidra.util.Msg;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.filechooser.GhidraFileChooserModel;
 import ghidra.util.filechooser.GhidraFileFilter;
@@ -321,14 +320,18 @@ public class BundleStatusComponentProvider extends ComponentProviderAdapter {
 	}
 
 	private void notifyTableRowChanged(BundleStatus status) {
+		Swing.runIfSwingOrRunLater(() -> {
 			int modelRowIndex = bundleStatusTableModel.getRowIndex(status);
 			int viewRowIndex = filterPanel.getViewRow(modelRowIndex);
 			bundleStatusTable
 					.notifyTableChanged(new TableModelEvent(bundleStatusTableModel, viewRowIndex));
+		});
 	}
 
 	private void notifyTableDataChanged() {
+		Swing.runIfSwingOrRunLater(() -> {
 			bundleStatusTable.notifyTableChanged(new TableModelEvent(bundleStatusTableModel));
+		});
 	}
 
 	@Override
@@ -374,7 +377,7 @@ public class BundleStatusComponentProvider extends ComponentProviderAdapter {
 		@Override
 		public void run(TaskMonitor monitor) throws CancelledException {
 			deactivateBundlesTask.run(monitor);
-			if (!monitor.isCancelled()) {
+			monitor.checkCanceled();
 			// partition bundles into system (bundles.get(true)) and non-system (bundles.get(false)).
 			Map<Boolean, List<GhidraBundle>> bundles = statuses.stream()
 					.map(bs -> bundleHost.getExistingGhidraBundle(bs.getFile()))
@@ -382,18 +385,16 @@ public class BundleStatusComponentProvider extends ComponentProviderAdapter {
 
 			List<GhidraBundle> systemBundles = bundles.get(true);
 			if (!systemBundles.isEmpty()) {
-					StringBuilder stringBuilder = new StringBuilder();
+				StringBuilder buff = new StringBuilder();
 				for (GhidraBundle bundle : systemBundles) {
-						stringBuilder.append(Path.toPathString(bundle.getFile()) + "\n");
+					buff.append(Path.toPathString(bundle.getFile()) + "\n");
 				}
 				Msg.showWarn(this, BundleStatusComponentProvider.this.getComponent(),
-						"Unabled to remove",
+					"Unabled to remove", "System bundles cannot be removed:\n" + buff.toString());
-						"System bundles cannot be removed:\n" + stringBuilder.toString());
 			}
 			bundleHost.remove(bundles.get(false));
 		}
 	}
-	}
 
 	private class EnableAndActivateBundlesTask extends Task {
 		private final List<BundleStatus> statuses;

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/osgi/GhidraBundleException.java

@@ -53,6 +53,18 @@ public class GhidraBundleException extends OSGiException {
 		this.bundleLocation = bundleLocation;
 	}
 
+	/**
+	 * Construct a new exception originating with the bundle having location identifier {@code bundleLocation}.
+	 * 
+	 * @param bundleLocation the bundle location identifier (since no bundle is available)
+	 * @param msg a contextual message
+	 */
+	public GhidraBundleException(String bundleLocation, String msg) {
+		super(msg);
+		this.bundle = null;
+		this.bundleLocation = bundleLocation;
+	}
+
 	/**
 	 * @return the associated bundle, or null.  If null, the bundle location identifier will be non-null
 	 */

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/osgi/GhidraJarBundle.java

@@ -23,11 +23,13 @@ import java.util.jar.Manifest;
 import java.util.stream.Collectors;
 
 import org.apache.felix.framework.util.manifestparser.ManifestParser;
+import org.osgi.framework.BundleException;
 import org.osgi.framework.wiring.BundleCapability;
 import org.osgi.framework.wiring.BundleRequirement;
 
 import aQute.bnd.osgi.Jar;
 import generic.jar.ResourceFile;
+import ghidra.util.exception.AssertException;
 
 /**
  * Proxy to an ordinary OSGi Jar bundle.  {@link GhidraJarBundle#build(PrintWriter)} does nothing.   
@@ -64,9 +66,12 @@ public class GhidraJarBundle extends GhidraBundle {
 		return bundleLocation;
 	}
 
-	protected ManifestParser createManifestParser() {
+	protected ManifestParser createManifestParser() throws GhidraBundleException {
 		try (Jar jar = new Jar(file.getFile(true))) {
 			Manifest manifest = jar.getManifest();
+			if (manifest == null) {
+				throw new GhidraBundleException(bundleLocation, "jar bundle with no manifest");
+			}
 			Attributes mainAttributes = manifest.getMainAttributes();
 			Map<String, Object> headerMap = mainAttributes.entrySet()
 					.stream()
@@ -74,8 +79,14 @@ public class GhidraJarBundle extends GhidraBundle {
 						Collectors.toMap(e -> e.getKey().toString(), e -> e.getValue().toString()));
 			return new ManifestParser(null, null, null, headerMap);
 		}
+		catch (BundleException e) {
+			throw new GhidraBundleException(bundleLocation, "parsing manifest", e);
+		}
+		catch (GhidraBundleException e) {
+			throw e;
+		}
 		catch (Exception e) {
-			throw new RuntimeException(e);
+			throw new AssertException("Unexpected exception while parsing manifest", e);
 		}
 	}
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/osgi/GhidraSourceBundle.java

@@ -713,11 +713,31 @@ public class GhidraSourceBundle extends GhidraBundle {
 			}
 		}
 		catch (Throwable e) {
-			Msg.error(this, "Exception searching ", e);
+			Msg.error(this, "Exception while searching for file system discrepancies ", e);
-			e.printStackTrace();
 		}
 	}
 
+	/* requirements that resolve internally are never "missing", but will only resolve _after_ build/install */
+	private boolean resolveInternally(List<BundleRequirement> requirements)
+			throws GhidraBundleException {
+		if (requirements.isEmpty()) {
+			return true;
+		}
+		List<BundleCapability> capabilities = getAllCapabilities();
+		Iterator<BundleRequirement> requirementIterator = requirements.iterator();
+		boolean anyMissing = false;
+		while (requirementIterator.hasNext()) {
+			BundleRequirement requirement = requirementIterator.next();
+			if (capabilities.stream().anyMatch(requirement::matches)) {
+				requirementIterator.remove();
+			}
+			else {
+				anyMissing = true;
+			}
+		}
+		return !anyMissing;
+	}
+
 	/*
 	 * when calling the java compiler programmatically, we map import requests to files with
 	 * a custom {@link JavaFileManager}.  We wrap the system JavaFileManager with one that
@@ -740,7 +760,7 @@ public class GhidraSourceBundle extends GhidraBundle {
 		List<BundleRequirement> requirements = getAllRequirements();
 		List<BundleWiring> bundleWirings = bundleHost.resolve(requirements);
 
-		if (!requirements.isEmpty()) {
+		if (!resolveInternally(requirements)) {
 			writer.printf("%d import requirement%s remain%s unresolved:\n", requirements.size(),
 				requirements.size() > 1 ? "s" : "", requirements.size() > 1 ? "" : "s");
 			for (BundleRequirement requirement : requirements) {
@@ -1097,8 +1117,7 @@ public class GhidraSourceBundle extends GhidraBundle {
 			}
 
 			try (Stream<Path> paths = Files.list(directory)) {
-				classToClassFilesMap = paths
+				classToClassFilesMap = paths.filter(p -> Files.isRegularFile(p))
-						.filter(p -> Files.isRegularFile(p))
 						.filter(p -> p.getFileName().toString().endsWith(".class"))
 						.collect(groupingBy(this::getClassName));
 			}

Ghidra/Features/Base/src/main/java/ghidra/app/util/bin/format/elf/ElfDefaultGotPltMarkup.java

@@ -122,20 +122,37 @@ public class ElfDefaultGotPltMarkup {
 			if (relocationTable == null) {
 				return;
 			}
-			ElfRelocation[] relocations = relocationTable.getRelocations();
-			int count = relocations.length;
 
-			// First few entries of GOT do not correspond to dynamic symbols.
+			// External dynamic symbol entries in the PLTGOT, if any, will be placed
-			// First relocation address must be used to calculate GOT end address
+			// after any local symbol entries.
-			// based upon the total number of relocation entries.
+
-			long firstGotEntryOffset = relocations[0].getOffset() + imageBaseAdj;
+			// While DT_PLTGOT identifies the start of the PLTGOT it does not
+			// specify its length.  If there are dynamic non-local entries in the 
+			// PLTGOT they should have relocation entries in the table identified 
+			// by DT_JMPREL.  It is important to note that this relocation table
+			// can include entries which affect other processor-specific PLTGOT
+			// tables (e.g., MIPS_PLTGOT) so we must attempt to isolate the 
+			// entries which correspond to DT_PLTGOT.  
+
+			// WARNING: This implementation makes a potentially bad assumption that 
+			// the last relocation entry will identify the endof the PLTGOT if its
+			// offset is beyond the start of the PLTGOT.  This assumption could
+			// easily be violated by a processor-specific PLTGOT which falls after
+			// the standard PLTGOT in memory and shares the same relocation table.
 
 			long pltgot = elf.adjustAddressForPrelink(
-				dynamicTable.getDynamicValue(ElfDynamicType.DT_PLTGOT)) + imageBaseAdj;
+				dynamicTable.getDynamicValue(ElfDynamicType.DT_PLTGOT));
+
+			ElfRelocation[] relocations = relocationTable.getRelocations();
+
+			long lastGotOffset = relocations[relocations.length - 1].getOffset();
+			if (lastGotOffset < pltgot) {
+				return;
+			}
+
+			Address gotStart = defaultSpace.getAddress(pltgot + imageBaseAdj);
+			Address gotEnd = defaultSpace.getAddress(lastGotOffset + imageBaseAdj);
 
-			Address gotStart = defaultSpace.getAddress(pltgot);
-			Address gotEnd = defaultSpace.getAddress(
-				firstGotEntryOffset + (count * defaultSpace.getPointerSize()) - 1);
 			processGOT(gotStart, gotEnd, monitor);
 			processDynamicPLT(gotStart, gotEnd, monitor);
 		}
@@ -162,7 +179,7 @@ public class ElfDefaultGotPltMarkup {
 
 		try {
 			Address newImageBase = null;
-			while (gotStart.compareTo(gotEnd) < 0) {
+			while (gotStart.compareTo(gotEnd) <= 0) {
 				monitor.checkCanceled();
 
 				Data data = createPointer(gotStart, true);
@@ -350,7 +367,7 @@ public class ElfDefaultGotPltMarkup {
 			return null;
 		}
 		int pointerSize = program.getDataTypeManager().getDataOrganization().getPointerSize();
-		Pointer pointer = PointerDataType.dataType;
+		Pointer pointer = PointerDataType.dataType.clone(program.getDataTypeManager());
 		if (elf.is32Bit() && pointerSize != 4) {
 			pointer = Pointer32DataType.dataType;
 		}
@@ -364,18 +381,48 @@ public class ElfDefaultGotPltMarkup {
 			}
 			data = listing.createData(addr, pointer);
 		}
-		Address refAddr = (Address) data.getValue();
+		if (keepRefWhenValid && isValidPointer(data)) {
-		if (keepRefWhenValid) {
+			setConstant(data);
-			if (memory.contains(refAddr)) {
+		}
+		else {
+			removeMemRefs(data);
+		}
 		return data;
 	}
+
+	/**
+	 * Set specified data as constant if contained within a writable block.  It can be helpful
+	 * to the decompiler results if constant pointers are marked as such (e.g., GOT entries)
+	 * @param data program data
+	 */
+	public static void setConstant(Data data) {
+		Memory memory = data.getProgram().getMemory();
+		MemoryBlock block = memory.getBlock(data.getAddress());
+		if (!block.isWrite() || block.getName().startsWith(ElfSectionHeaderConstants.dot_got)) {
+			// .got blocks will be force to read-only by ElfDefaultGotPltMarkup
+			return;
+		}
+		data.setLong(MutabilitySettingsDefinition.MUTABILITY,
+			MutabilitySettingsDefinition.CONSTANT);
+	}
+
+	/**
+	 * Determine if pointerData refers to a valid memory address or symbol
+	 * @param pointerData pointer data
+	 * @return true if pointer data refers to valid memory address or symbol
+	 */
+	public static boolean isValidPointer(Data pointerData) {
+		Program program = pointerData.getProgram();
+		Memory memory = program.getMemory();
+		Address refAddr = (Address) pointerData.getValue();
+		if (memory.contains(refAddr)) {
+			return true;
+		}
 		Symbol syms[] = program.getSymbolTable().getSymbols(refAddr);
 		if (syms != null && syms.length > 0 && syms[0].getSource() != SourceType.DEFAULT) {
-				return data;
+			return true;
 		}
-		}
+		return false;
-		removeMemRefs(data);
-		return data;
 	}
 
 	private void removeMemRefs(Data data) {

Ghidra/Features/Base/src/main/java/ghidra/app/util/navigation/GoToServiceImpl.java

@@ -105,7 +105,7 @@ public class GoToServiceImpl implements GoToService {
 			programLocation = override.goTo(goToAddress);
 		}
 		if (programLocation == null) {
-			programLocation = helper.getProgramLocationForAddress(goToAddress, program);
+			programLocation = GoToHelper.getProgramLocationForAddress(goToAddress, program);
 		}
 		else {
 			program = programLocation.getProgram();
@@ -116,7 +116,7 @@ public class GoToServiceImpl implements GoToService {
 
 	@Override
 	public boolean goTo(Address goToAddress, Program program) {
-		ProgramLocation location = helper.getProgramLocationForAddress(goToAddress, program);
+		ProgramLocation location = GoToHelper.getProgramLocationForAddress(goToAddress, program);
 		return helper.goTo(defaultNavigatable, location, program);
 	}
 

Ghidra/Features/Decompiler/src/main/java/ghidra/app/plugin/core/decompile/actions/AbstractDecompilerAction.java

@@ -100,9 +100,6 @@ public abstract class AbstractDecompilerAction extends DockingAction {
 		HighVariable variable = token.getHighVariable();
 		HighSymbol highSymbol = null;
 		if (variable == null) {
-			if (highFunction == null) {
-				return null;
-			}
 			// Token may be from a variable reference, in which case we have to dig to find the actual symbol
 			Function function = highFunction.getFunction();
 			if (function == null) {

Ghidra/Features/Decompiler/src/test.slow/java/ghidra/app/plugin/core/decompile/DecompilerClangTest.java

@@ -945,14 +945,14 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 	private void refresh() {
 
 		DockingActionIf action = getAction(decompiler, "Refresh");
-		performAction(action);
+		performAction(action, provider.getActionContext(null), true);
 		waitForDecompiler();
 	}
 
 	private DecompilerProvider cloneDecompiler() {
 
 		DockingActionIf action = getAction(decompiler, "Decompile Clone");
-		performAction(action);
+		performAction(action, provider.getActionContext(null), true);
 		waitForSwing();
 
 		@SuppressWarnings("unchecked")
@@ -1035,7 +1035,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 
 	private void backwardSlice() {
 		DockingActionIf action = getAction(decompiler, BackwardsSliceAction.NAME);
-		performAction(action);
+		performAction(action, provider.getActionContext(null), true);
 	}
 
 	private void middleMouse() {
@@ -1064,7 +1064,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 
 	private void rename(String newName) {
 		DockingActionIf action = getAction(decompiler, "Rename Variable");
-		performAction(action, false);
+		performAction(action, provider.getActionContext(null), false);
 
 		InputDialog dialog = waitForDialogComponent(InputDialog.class);
 		runSwing(() -> dialog.setValue(newName));
@@ -1077,7 +1077,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 
 		DockingActionIf highlightAction =
 			getAction(decompiler, RemoveAllSecondaryHighlightsAction.NAME);
-		performAction(highlightAction);
+		performAction(highlightAction, provider.getActionContext(null), true);
 	}
 
 	private Color highlight() {
@@ -1085,7 +1085,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 		ClangToken token = getToken();
 
 		DockingActionIf highlightAction = getAction(decompiler, SetSecondaryHighlightAction.NAME);
-		performAction(highlightAction);
+		performAction(highlightAction, provider.getActionContext(null), true);
 
 		HighlightToken ht = getSecondaryHighlight(token);
 		assertNotNull("No highlight for token: " + token, ht);
@@ -1106,7 +1106,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 
 		DockingActionIf highlightAction =
 			getAction(decompiler, SetSecondaryHighlightColorChooserAction.NAME);
-		performAction(highlightAction, false);
+		performAction(highlightAction, provider.getActionContext(null), false);
 
 		Window w = waitForWindow("Please Choose a Color");
 		GhidraColorChooser colorChooser = findComponent(w, GhidraColorChooser.class);
@@ -1238,7 +1238,7 @@ public class DecompilerClangTest extends AbstractDecompilerTest {
 		for (DockingActionIf action : actions) {
 			Object service = getInstanceField("clipboardService", action);
 			if (service.getClass().toString().contains("Decomp")) {
-				performAction(action);
+				performAction(action, provider.getActionContext(null), true);
 				return;
 			}
 		}

Ghidra/Features/FunctionGraph/src/test/java/ghidra/app/plugin/core/functiongraph/AbstractFunctionGraphTest.java

@@ -2166,12 +2166,6 @@ public abstract class AbstractFunctionGraphTest extends AbstractGhidraHeadedInte
 		Double scale = getGraphScale(getPrimaryGraphViewer());
 		int result = Double.compare(scale, 1.0);
 		assertEquals("Graph not fully zoomed-in; scale: " + scale, 0, result);
-
-		FGVertex v = getFocusedVertex();
-		Rectangle cursorBounds = v.getCursorBounds();
-		Window graphWindow = windowForComponent(getPrimaryGraphViewer());
-		Rectangle windowBounds = graphWindow.getBounds();
-		assertTrue(windowBounds.contains(cursorBounds));
 	}
 
 	protected void assertZoomedOut() {
@@ -2277,7 +2271,7 @@ public abstract class AbstractFunctionGraphTest extends AbstractGhidraHeadedInte
 
 	protected void goTo(Address address) {
 		GoToService goToService = tool.getService(GoToService.class);
-		goToService.goTo(address);
+		runSwing(() -> goToService.goTo(address));
 		waitForBusyGraph();
 	}
 

Ghidra/Features/FunctionGraph/src/test/java/ghidra/app/plugin/core/functiongraph/FunctionGraphPlugin1Test.java

@@ -843,7 +843,7 @@ public class FunctionGraphPlugin1Test extends AbstractFunctionGraphTest {
 	private void setNavigationHistoryOption(NavigationHistoryChoices choice) throws Exception {
 		FGController controller = getFunctionGraphController();
 		FunctionGraphOptions options = controller.getFunctionGraphOptions();
-		setInstanceField("navigationHistoryChoice", options, choice);
+		runSwing(() -> setInstanceField("navigationHistoryChoice", options, choice));
 		waitForSwing();
 	}
 

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/DefaultGraphDisplay.java

@@ -64,6 +64,7 @@ import ghidra.graph.job.GraphJobRunner;
 import ghidra.service.graph.*;
 import ghidra.util.*;
 import ghidra.util.exception.CancelledException;
+import ghidra.util.task.TaskLauncher;
 import ghidra.util.task.TaskMonitor;
 import resources.Icons;
 
@@ -128,10 +129,6 @@ public class DefaultGraphDisplay implements GraphDisplay {
 	 * provides graph displays for supplied graphs
 	 */
 	private final DefaultGraphDisplayProvider graphDisplayProvider;
-	/**
-	 *  a 'busy' dialog to show while the layout algorithm is working
-	 */
-	private LayoutWorkingDialog layoutWorkingDialog;
 	/**
 	 * the vertex that has been nominated to be 'focused' in the graph display and listing
 	 */
@@ -359,20 +356,6 @@ public class DefaultGraphDisplay implements GraphDisplay {
 				.onActionStateChanged((s, t) -> layoutChanged(s.getName()))
 				.addStates(getLayoutActionStates())
 				.buildAndInstallLocal(componentProvider);
-
-		// show a 'busy' dialog while the layout algorithm is computing vertex locations
-		viewer.getVisualizationModel()
-				.getLayoutModel()
-				.getLayoutStateChangeSupport()
-				.addLayoutStateChangeListener(
-					evt -> {
-						if (evt.active) {
-							Swing.runLater(this::showLayoutWorking);
-						}
-						else {
-							Swing.runLater(this::hideLayoutWorking);
-						}
-					});
 	}
 
 	private void createPopupActions() {
@@ -569,7 +552,8 @@ public class DefaultGraphDisplay implements GraphDisplay {
 	 */
 	private void layoutChanged(String layoutName) {
 		if (layoutTransitionManager != null) {
-			layoutTransitionManager.setLayout(layoutName);
+			new TaskLauncher(new SetLayoutTask(viewer, layoutTransitionManager, layoutName), null,
+				1000);
 		}
 	}
 
@@ -587,27 +571,6 @@ public class DefaultGraphDisplay implements GraphDisplay {
 		componentProvider.getTool().showDialog(filterDialog);
 	}
 
-	/**
-	 * show the 'busy' dialog indicating that the layout algorithm is working
-	 */
-	protected void showLayoutWorking() {
-		if (this.layoutWorkingDialog != null) {
-			layoutWorkingDialog.close();
-		}
-		this.layoutWorkingDialog =
-			new LayoutWorkingDialog(viewer.getVisualizationModel().getLayoutAlgorithm());
-		componentProvider.getTool().showDialog(layoutWorkingDialog);
-	}
-
-	/**
-	 * hide the 'busy' dialog for the layout algorithm work
-	 */
-	protected void hideLayoutWorking() {
-		if (this.layoutWorkingDialog != null) {
-			layoutWorkingDialog.close();
-		}
-	}
-
 	/**
 	 * add or remove the satellite viewer
 	 * @param context information about the event
@@ -1216,7 +1179,7 @@ public class DefaultGraphDisplay implements GraphDisplay {
 
 	@Override
 	public void addAction(DockingAction action) {
-		componentProvider.addLocalAction(action);
+		Swing.runLater(() -> componentProvider.addLocalAction(action));
 	}
 
 	@Override
@@ -1286,4 +1249,19 @@ public class DefaultGraphDisplay implements GraphDisplay {
 	public AttributedGraph getGraph() {
 		return graph;
 	}
+
+	/**
+	 * Removes all externally added actions. This is called before re-using the graph window for a
+	 * new graph which may add its own set of actions for that particular graph.
+	 */
+	void restoreToDefaultSetOfActions() {
+		Swing.runLater(() -> {
+			// remove all actions
+			componentProvider.removeAllLocalActions();
+			// put the standard graph actions back
+			createToolbarActions();
+			createPopupActions();
+		});
+	}
+
 }

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/DefaultGraphDisplayComponentProvider.java

@@ -69,4 +69,10 @@ public class DefaultGraphDisplayComponentProvider extends ComponentProviderAdapt
 	public ActionContext getActionContext(MouseEvent event) {
 		return display.getActionContext(event);
 	}
+
+	// overridden to make it accessible
+	@Override
+	public void removeAllLocalActions() {
+		super.removeAllLocalActions();
+	}
 }

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/DefaultGraphDisplayProvider.java

@@ -51,7 +51,9 @@ public class DefaultGraphDisplayProvider implements GraphDisplayProvider {
 			TaskMonitor monitor) {
 
 		if (reuseGraph && !displays.isEmpty()) {
-			return getVisibleGraph();
+			DefaultGraphDisplay visibleGraph = getVisibleGraph();
+			visibleGraph.restoreToDefaultSetOfActions();
+			return visibleGraph;
 		}
 
 		DefaultGraphDisplay display =
@@ -73,9 +75,11 @@ public class DefaultGraphDisplayProvider implements GraphDisplayProvider {
 	 * return one from the Set via its iterator
 	 * @return a display that is showing
 	 */
-	private GraphDisplay getVisibleGraph() {
+	private DefaultGraphDisplay getVisibleGraph() {
-		return displays.stream().filter(d -> d.getComponent().isShowing())
+		return displays.stream()
-				.findAny().orElse(displays.iterator().next());
+				.filter(d -> d.getComponent().isShowing())
+				.findAny()
+				.orElse(displays.iterator().next());
 	}
 
 	@Override
@@ -100,4 +104,5 @@ public class DefaultGraphDisplayProvider implements GraphDisplayProvider {
 	public void remove(DefaultGraphDisplay defaultGraphDisplay) {
 		displays.remove(defaultGraphDisplay);
 	}
+
 }

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/LayoutWorkingDialog.java

@@ -1,57 +0,0 @@
-/* ###
- * IP: GHIDRA
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- * 
- *      http://www.apache.org/licenses/LICENSE-2.0
- * 
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-package ghidra.graph.visualization;
-
-import java.awt.BorderLayout;
-
-import javax.swing.*;
-
-import org.jungrapht.visualization.layout.algorithms.LayoutAlgorithm;
-
-import docking.DialogComponentProvider;
-import ghidra.service.graph.AttributedVertex;
-
-/**
- * Extends DialogComponentProvider to make a dialog with buttons to show that the
- * layout arrangement algorithm is busy
- */
-public class LayoutWorkingDialog extends DialogComponentProvider {
-
-	public LayoutWorkingDialog(LayoutAlgorithm<AttributedVertex> layoutAlgorithm) {
-		super("Working....", false);
-		super.addWorkPanel(createPanel(layoutAlgorithm));
-		setRememberSize(false);
-		addDismissButton();
-		setDefaultButton(dismissButton);
-	}
-
-	/**
-	 * Create a layout-formatted JComponent holding 2 vertical lists
-	 * of buttons, one list for vertex filter buttons and one list for
-	 * edge filter buttons. Each list has a border and title.
-	 * @return a formatted JComponent (container)
-	 */
-	JComponent createPanel(LayoutAlgorithm<AttributedVertex> layoutAlgorithm) {
-		JProgressBar progressBar = new JProgressBar();
-		progressBar.setIndeterminate(true);
-		JPanel panel = new JPanel(new BorderLayout());
-		panel.add(progressBar, BorderLayout.CENTER);
-		panel.add(new JLabel("Please wait......."), BorderLayout.NORTH);
-		addCancelButton();
-		cancelButton.addActionListener(evt -> layoutAlgorithm.cancel());
-		return panel;
-	}
-}

Ghidra/Features/GraphServices/src/main/java/ghidra/graph/visualization/SetLayoutTask.java

@@ -0,0 +1,106 @@
+/* ###
+ * IP: GHIDRA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package ghidra.graph.visualization;
+
+import java.util.concurrent.CountDownLatch;
+
+import org.jungrapht.visualization.VisualizationModel;
+import org.jungrapht.visualization.VisualizationViewer;
+import org.jungrapht.visualization.layout.event.LayoutStateChange.*;
+import org.jungrapht.visualization.layout.model.LayoutModel;
+
+import ghidra.service.graph.AttributedEdge;
+import ghidra.service.graph.AttributedVertex;
+import ghidra.util.Swing;
+import ghidra.util.exception.CancelledException;
+import ghidra.util.task.*;
+
+/**
+ * Task to change the layout of the graph
+ */
+public class SetLayoutTask extends Task {
+
+	private LayoutTransitionManager layoutTransitionManager;
+	private String layoutName;
+	private VisualizationViewer<AttributedVertex, AttributedEdge> viewer;
+	private CountDownLatch taskDone = new CountDownLatch(1);
+
+	public SetLayoutTask(VisualizationViewer<AttributedVertex, AttributedEdge> viewer,
+			LayoutTransitionManager layoutTransitionManager, String layoutName) {
+		super("Changing Graph Layout to " + layoutName, true, false, true, false);
+		this.viewer = viewer;
+		this.layoutTransitionManager = layoutTransitionManager;
+		this.layoutName = layoutName;
+	}
+
+	@Override
+	public void run(TaskMonitor monitor) throws CancelledException {
+		// add a callback for when/if the user cancels the layout, use a variable cause
+		// monitor uses a weak listener list and it would othewise get garbage collected.
+		CancelledListener cancelListener = this::taskCancelled;
+		monitor.addCancelledListener(cancelListener);
+
+		// add a listener so we are notified when the layout starts and ends
+		VisualizationModel<AttributedVertex, AttributedEdge> model = viewer.getVisualizationModel();
+		LayoutModel<AttributedVertex> layoutModel = model.getLayoutModel();
+		Support support = layoutModel.getLayoutStateChangeSupport();
+		Listener listener = this::layoutStateChanged;
+		support.addLayoutStateChangeListener(listener);
+
+		// start the layout - needs to be done on swing thread to prevent issues and intermediate 
+		// paints - should be changed in the future to not require it to be on the swing thread.
+		Swing.runNow(() -> layoutTransitionManager.setLayout(layoutName));
+
+		// some of the layouts are done on the calling thread and some aren't. If they are on 
+		// the calling thread, then by now, we already got the "done" callback and the "taskDone"
+		// countdown latch has been triggered and won't wait.  If, however, the layout has been
+		// diverted to another thread, we want to wait until the layout is completed
+		// There are two ways the latch will be triggered, the layout is completed or the user
+		// cancles the layout.
+		try {
+			taskDone.await();
+		}
+		catch (InterruptedException e) {
+			model.getLayoutAlgorithm().cancel();
+		}
+
+		// clean up the listeners
+		support.removeLayoutStateChangeListener(listener);
+		monitor.removeCancelledListener(cancelListener);
+	}
+
+	/**
+	 * Notfication when the layout algorithm starts and stops.
+	 * @param e the event. If the event.active is true, then the
+	 * algorithm is starting, if false, the algorithm is done.
+	 */
+	private void layoutStateChanged(Event e) {
+		if (!e.active) {
+			// algorithm is done, release the latch
+			taskDone.countDown();
+		}
+	}
+
+	/**
+	 * Callback if the user cancels the layout
+	 */
+	private void taskCancelled() {
+		// release the latch and tell the layout algorithm to cancel.
+		taskDone.countDown();
+		viewer.getVisualizationModel().getLayoutAlgorithm().cancel();
+	}
+
+}

Ghidra/Framework/Docking/src/main/java/docking/ComponentProvider.java

@@ -267,7 +267,7 @@ public abstract class ComponentProvider implements HelpDescriptor, ActionContext
 	}
 
 	/**
-	 * Removes the given action from the system.
+	 * Removes the given action from this component provider.
 	 * @param action The action to remove.
 	 */
 	protected void removeLocalAction(DockingAction action) {
@@ -277,6 +277,16 @@ public abstract class ComponentProvider implements HelpDescriptor, ActionContext
 		}
 	}
 
+	/**
+	 * Removes all local actions from this component provider
+	 */
+	protected void removeAllLocalActions() {
+		if (isInTool()) {
+			actionSet.forEach(action -> dockingTool.removeLocalAction(this, action));
+		}
+		actionSet.clear();
+	}
+
 	/**
 	 * Convenience method to show or hide this provider.
 	 * @param visible True shows the provider; false hides the provider

Ghidra/Framework/Docking/src/main/java/docking/widgets/fieldpanel/support/HoverProvider.java

@@ -24,6 +24,7 @@ public interface HoverProvider {
 
 	/**
 	 * Returns true if this service's popup window is currently visible
+	 * @return true if this service's popup window is currently visible
 	 */
 	public boolean isShowing();
 

Ghidra/Framework/Docking/src/main/java/ghidra/util/task/TaskMonitorComponent.java

@@ -273,6 +273,7 @@ public class TaskMonitorComponent extends JPanel implements TaskMonitor {
 	 * @return true if {@link #setIndeterminate(boolean)} with a value of <code>true</code> has
 	 * been called.
 	 */
+	@Override
 	public boolean isIndeterminate() {
 		return isIndeterminate.get();
 	}

Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/model/data/DataUtilities.java

@@ -125,7 +125,13 @@ public final class DataUtilities {
 			existingDataLen = data.getLength();
 			existingDT = data.getDataType();
 
+			if (data.isDefined() && newDataType.isEquivalent(existingDT)) {
+				return data;
+			}
+
 			// Check for external reference on pointer
+			if (existingDT instanceof Pointer) {
+				// TODO: This can probably be eliminated
 				Reference[] refs = refMgr.getReferencesFrom(addr);
 				for (Reference ref : refs) {
 					if (ref.getOperandIndex() == 0 && ref.isExternalReference()) {
@@ -134,6 +140,7 @@ public final class DataUtilities {
 					}
 				}
 			}
+		}
 
 		newDataType = newDataType.clone(program.getDataTypeManager());
 		newDataType = reconcileAppliedDataType(existingDT, newDataType, stackPointers);
@@ -192,11 +199,11 @@ public final class DataUtilities {
 	private static void checkEnoughSpace(Program program, Address addr, int existingDataLen,
 			DataTypeInstance dti, ClearDataMode mode) throws CodeUnitInsertionException {
 		Listing listing = program.getListing();
-		int newSize = dti.getLength();
+//		int newSize = dti.getLength();
-		if (newSize <= existingDataLen) {
+//		if (newSize <= existingDataLen) {
-			listing.clearCodeUnits(addr, addr, false);
+//			listing.clearCodeUnits(addr, addr, false);
-			return;
+//			return;
-		}
+//		}
 		try {
 			Address end = addr.addNoWrap(existingDataLen - 1);
 			Address newEnd = addr.addNoWrap(dti.getLength() - 1);

Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/model/data/PointerDataType.java

@@ -60,7 +60,7 @@ public class PointerDataType extends BuiltIn implements Pointer {
 	 * organization when resolved.
 	 */
 	public PointerDataType() {
-		this(null, -1, null);
+		this(DataType.DEFAULT, -1, null);
 	}
 
 	/**
@@ -72,7 +72,7 @@ public class PointerDataType extends BuiltIn implements Pointer {
 	 * @param dtm data-type manager whose data organization should be used
 	 */
 	public PointerDataType(DataTypeManager dtm) {
-		this(null, -1, dtm);
+		this(DataType.DEFAULT, -1, dtm);
 	}
 
 	/**
@@ -142,7 +142,7 @@ public class PointerDataType extends BuiltIn implements Pointer {
 	}
 
 	@Override
-	public final DataType clone(DataTypeManager dtm) {
+	public final Pointer clone(DataTypeManager dtm) {
 		if (dtm == getDataTypeManager()) {
 			return this;
 		}

Ghidra/Processors/MIPS/src/main/java/ghidra/app/util/bin/format/elf/extend/MIPS_ElfExtension.java

@@ -744,7 +744,9 @@ public class MIPS_ElfExtension extends ElfExtension {
 				Address gotEntryAddr =
 					adjustTableEntryIfNonZero(gotBaseAddress, i, imageShift, elfLoadHelper);
 				Data pointerData = elfLoadHelper.createData(gotEntryAddr, PointerDataType.dataType);
-				setConstant(pointerData);
+				if (ElfDefaultGotPltMarkup.isValidPointer(pointerData)) {
+					ElfDefaultGotPltMarkup.setConstant(pointerData);
+				}
 			}
 
 			// process global/external symbol got entries
@@ -753,7 +755,7 @@ public class MIPS_ElfExtension extends ElfExtension {
 				Address gotEntryAddr = adjustTableEntryIfNonZero(gotBaseAddress, gotIndex++,
 					imageShift, elfLoadHelper);
 				Data pointerData = elfLoadHelper.createData(gotEntryAddr, PointerDataType.dataType);
-				setConstant(pointerData);
+				ElfDefaultGotPltMarkup.setConstant(pointerData);
 				if (elfSymbols[i].isFunction() && elfSymbols[i].getSectionHeaderIndex() == 0) {
 					// ensure that external function/thunk are created in absence of sections
 					Address refAddr = (Address) pointerData.getValue();
@@ -811,7 +813,7 @@ public class MIPS_ElfExtension extends ElfExtension {
 				Address gotEntryAddr = adjustTableEntryIfNonZero(mipsPltgotBase, ++gotEntryIndex,
 					imageShift, elfLoadHelper);
 				Data pointerData = elfLoadHelper.createData(gotEntryAddr, PointerDataType.dataType);
-				setConstant(pointerData);
+				ElfDefaultGotPltMarkup.setConstant(pointerData);
 			}
 		}
 		catch (NotFoundException e) {
@@ -822,17 +824,6 @@ public class MIPS_ElfExtension extends ElfExtension {
 		}
 	}
 
-	private void setConstant(Data pointerData) {
-		Memory memory = pointerData.getProgram().getMemory();
-		MemoryBlock block = memory.getBlock(pointerData.getAddress());
-		if (!block.isWrite() || block.getName().startsWith(ElfSectionHeaderConstants.dot_got)) {
-			// .got blocks will be force to read-only by ElfDefaultGotPltMarkup
-			return;
-		}
-		pointerData.setLong(MutabilitySettingsDefinition.MUTABILITY,
-			MutabilitySettingsDefinition.CONSTANT);
-	}
-
 	private Address adjustTableEntryIfNonZero(Address tableBaseAddr, int entryIndex,
 			long adjustment, ElfLoadHelper elfLoadHelper) throws MemoryAccessException {
 		boolean is64Bit = elfLoadHelper.getElfHeader().is64Bit();

Ghidra/Processors/PowerPC/src/main/java/ghidra/app/util/bin/format/elf/extend/PowerPC64_ElfExtension.java

@@ -368,6 +368,9 @@ public class PowerPC64_ElfExtension extends ElfExtension {
 			return null;
 		}
 
+		ElfDefaultGotPltMarkup.setConstant(refPtr);
+		ElfDefaultGotPltMarkup.setConstant(tocPtr);
+
 		Function function = program.getListing().getFunctionAt(refAddr);
 		if (function == null) {
 			// Check for potential pointer table (unsure a non-function would be referenced by OPD section)