Merge remote-tracking branch 'origin/patch'

Ghidra/Features/Base/src/main/java/ghidra/app/merge/datatypes/DataTypeMergeManager.java

@@ -268,11 +268,11 @@ public class DataTypeMergeManager implements MergeResolver {
 
 	private void processSourceArchiveChanges() throws CancelledException {
 		conflictOption = OPTION_MY;
-		for (int i = 0; i < myArchiveChangeList.size(); i++) {
+		for (Long element : myArchiveChangeList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = myArchiveChangeList.get(i).longValue();
+			long id = element.longValue();
 
 			updateSourceArchive(id);
 		}
@@ -318,11 +318,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	}
 
 	private void processSourceArchiveAdditions() throws CancelledException {
-		for (int i = 0; i < myArchiveAddedList.size(); i++) {
+		for (Long element : myArchiveAddedList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = myArchiveAddedList.get(i).longValue();
+			long id = element.longValue();
 
 			UniversalID universalID = new UniversalID(id);
 			SourceArchive mySourceArchive = dtms[MY].getSourceArchive(universalID);
@@ -381,11 +381,11 @@ public class DataTypeMergeManager implements MergeResolver {
 
 	private void processSourceArchiveConflicts() throws CancelledException {
 
-		for (int i = 0; i < archiveConflictList.size(); i++) {
+		for (Long element : archiveConflictList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long sourceArchiveID = archiveConflictList.get(i).longValue();
+			long sourceArchiveID = element.longValue();
 
 			++currentConflictIndex;
 			handleSourceArchiveConflict(sourceArchiveID, currentConflictIndex);
@@ -412,11 +412,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	 * @throws CancelledException if task cancelled
 	 */
 	private void processCategoriesAdded() throws CancelledException {
-		for (int i = 0; i < myCatAddedList.size(); i++) {
+		for (Long element : myCatAddedList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = myCatAddedList.get(i).longValue();
+			long id = element.longValue();
 			Category myCat = dtms[MY].getCategory(id);
 			CategoryPath myPath = myCat.getCategoryPath();
 			if (dtms[RESULT].containsCategory(myPath)) {
@@ -432,11 +432,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	 */
 	private void processCategoryConflicts() throws CancelledException {
 
-		for (int i = 0; i < catConflictList.size(); i++) {
+		for (Long element : catConflictList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = catConflictList.get(i).longValue();
+			long id = element.longValue();
 
 			++currentConflictIndex;
 			handleCategoryConflict(id, currentConflictIndex);
@@ -460,11 +460,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	}
 
 	private void processCategoryChanges() throws CancelledException {
-		for (int i = 0; i < myCatChangeList.size(); i++) {
+		for (Long element : myCatChangeList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = myCatChangeList.get(i).longValue();
+			long id = element.longValue();
 
 			processCategoryRenamed(id);
 			processCategoryMoved(id);
@@ -473,10 +473,10 @@ public class DataTypeMergeManager implements MergeResolver {
 	}
 
 	private void processCategoriesDeleted() throws CancelledException {
-		for (int i = 0; i < myCatChangeList.size(); i++) {
+		for (Long element : myCatChangeList) {
 			currentMonitor.checkCanceled();
 
-			long id = myCatChangeList.get(i).longValue();
+			long id = element.longValue();
 			processCategoryDeleted(id);
 		}
 	}
@@ -499,8 +499,7 @@ public class DataTypeMergeManager implements MergeResolver {
 		if (fixUpList.size() > 0) {
 			StringBuffer sb = new StringBuffer();
 			sb.append("The following data types are unresolved:\n");
-			for (int i = 0; i < fixUpList.size(); i++) {
+			for (FixUpInfo info : fixUpList) {
-				FixUpInfo info = fixUpList.get(i);
 				DataTypeManager dtm = info.getDataTypeManager();
 				DataType dt = dtm.getDataType(info.id);
 				DataType compDt = dtm.getDataType(info.compID);
@@ -1128,15 +1127,15 @@ public class DataTypeMergeManager implements MergeResolver {
 				fixUpList.add(new FixUpInfo(sourceDtID, sourceComponentID, Integer.MAX_VALUE,
 					resolvedDataTypes));
 				fixUpIDSet.add(sourceDtID);
+
+				// substitute datatype to preserve component name for subsequent fixup
+				resultCompDt = Undefined1DataType.dataType;
 			}
 		}
 		try {
-			if (resultCompDt != null) {
+			// Apply resultCompDt as flex array
-				// There is a matching component data type in the result.
 			try {
-					// If I have compDt, it should now be from result DTM.
+				destStruct.setFlexibleArrayComponent(resultCompDt, flexDtc.getFieldName(), comment);
-					destStruct.setFlexibleArrayComponent(resultCompDt, flexDtc.getFieldName(),
-						comment);
 			}
 			catch (IllegalArgumentException e) {
 				displayError(destStruct, e);
@@ -1146,10 +1145,6 @@ public class DataTypeMergeManager implements MergeResolver {
 				destStruct.setFlexibleArrayComponent(badDt, flexDtc.getFieldName(), comment);
 			}
 		}
-			else {
-				destStruct.clearFlexibleArrayComponent();
-			}
-		}
 		catch (IllegalArgumentException e) {
 			displayError(destStruct, e);
 		}
@@ -1216,7 +1211,9 @@ public class DataTypeMergeManager implements MergeResolver {
 					}
 					else {
 						// must have been deleted in LATEST
-						// put an entry in the fixup list if this is a conflict
+						// put an entry in the fixup list if this is a conflict.
+						// NOTE: This may also be caused by a replaced datatype but 
+						// we have no indication as to what the replacment was
 						deletedInLatest = true;
 					}
 				}
@@ -1599,11 +1596,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	 */
 	private void processDataTypeChanges() throws CancelledException {
 
-		for (int i = 0; i < myDtChangeList.size(); i++) {
+		for (Long element : myDtChangeList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long id = myDtChangeList.get(i).longValue();
+			long id = element.longValue();
 
 			DataType dt = dtms[MY].getDataType(id);
 			if ((dt instanceof Pointer) || (dt instanceof Array) || (dt instanceof BuiltIn)) {
@@ -1681,8 +1678,7 @@ public class DataTypeMergeManager implements MergeResolver {
 	}
 
 	private boolean isParent(CategoryPath catPath) {
-		for (int i = 0; i < myDtAddedList.size(); i++) {
+		for (Long id : myDtAddedList) {
-			Long id = myDtAddedList.get(i);
 			DataType dt = dtms[MY].getDataType(id.longValue());
 			if (catPath.equals(dt.getCategoryPath())) {
 				return true;
@@ -2225,10 +2221,10 @@ public class DataTypeMergeManager implements MergeResolver {
 	}
 
 	private void processDataTypesDeleted() throws CancelledException {
-		for (int i = 0; i < myDtChangeList.size(); i++) {
+		for (Long element : myDtChangeList) {
 			currentMonitor.checkCanceled();
 
-			long id = myDtChangeList.get(i).longValue();
+			long id = element.longValue();
 			processDataTypeDeleted(id);
 		}
 	}
@@ -2237,11 +2233,11 @@ public class DataTypeMergeManager implements MergeResolver {
 	 * 
 	 */
 	private void processDataTypesAdded() throws CancelledException {
-		for (int i = 0; i < myDtAddedList.size(); i++) {
+		for (Long element : myDtAddedList) {
 			currentMonitor.checkCanceled();
 			currentMonitor.setProgress(++progressIndex);
 
-			long myDtKey = myDtAddedList.get(i).longValue();
+			long myDtKey = element.longValue();
 			DataType myDt = dtms[MY].getDataType(myDtKey);
 
 			if (equivalentDataTypeFound(myDtKey, myDt)) {
@@ -3360,7 +3356,7 @@ public class DataTypeMergeManager implements MergeResolver {
 				if (nextOrdinal > maxOrdinal) {
 					break;
 				}
-				struct.getComponent(nextOrdinal);
+				dtc = struct.getComponent(nextOrdinal);
 			}
 			return null;
 		}

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

@@ -22,7 +22,6 @@ import java.util.*;
 import java.util.Map.Entry;
 import java.util.concurrent.CopyOnWriteArrayList;
 import java.util.concurrent.CountDownLatch;
-import java.util.function.Function;
 import java.util.stream.Collectors;
 
 import org.apache.felix.framework.FrameworkFactory;
@@ -63,8 +62,7 @@ public class BundleHost {
 	private static final String SAVE_STATE_TAG_ACTIVE = "BundleHost_ACTIVE";
 	private static final String SAVE_STATE_TAG_SYSTEM = "BundleHost_SYSTEM";
 
-	Map<ResourceFile, GhidraBundle> fileToBundleMap = new HashMap<>();
+	private final BundleMap bundleMap = new BundleMap();
-	Map<String, GhidraBundle> bundleLocationToBundleMap = new HashMap<>();
 
 	BundleContext frameworkBundleContext;
 	Framework felixFramework;
@@ -93,7 +91,7 @@ public class BundleHost {
 	 * @return false if the bundle was already enabled
 	 */
 	public boolean enable(ResourceFile bundleFile) {
-		GhidraBundle bundle = fileToBundleMap.get(bundleFile);
+		GhidraBundle bundle = bundleMap.get(bundleFile);
 		if (bundle == null) {
 			bundle = add(bundleFile, true, false);
 			return true;
@@ -139,7 +137,7 @@ public class BundleHost {
 	 * @return a {@link GhidraBundle} or {@code null}
 	 */
 	public GhidraBundle getExistingGhidraBundle(ResourceFile bundleFile) {
-		GhidraBundle bundle = fileToBundleMap.get(bundleFile);
+		GhidraBundle bundle = bundleMap.get(bundleFile);
 		if (bundle == null) {
 			Msg.showError(this, null, "ghidra bundle cache",
 				"getExistingGhidraBundle expected a GhidraBundle created at " + bundleFile +
@@ -156,7 +154,7 @@ public class BundleHost {
 	 * @return a {@link GhidraBundle} or {@code null}
 	 */
 	public GhidraBundle getGhidraBundle(ResourceFile bundleFile) {
-		return fileToBundleMap.get(bundleFile);
+		return bundleMap.get(bundleFile);
 	}
 
 	private static GhidraBundle createGhidraBundle(BundleHost bundleHost, ResourceFile bundleFile,
@@ -189,25 +187,11 @@ public class BundleHost {
 	 */
 	public GhidraBundle add(ResourceFile bundleFile, boolean enabled, boolean systemBundle) {
 		GhidraBundle bundle = createGhidraBundle(this, bundleFile, enabled, systemBundle);
-		fileToBundleMap.put(bundleFile, bundle);
+		bundleMap.add(bundle);
-		bundleLocationToBundleMap.put(bundle.getLocationIdentifier(), bundle);
 		fireBundleAdded(bundle);
 		return bundle;
 	}
 
-	private Set<ResourceFile> dedupeBundleFiles(List<ResourceFile> bundleFiles) {
-		Set<ResourceFile> dedupedBundleFiles = new HashSet<>(bundleFiles);
-		Iterator<ResourceFile> bundleFileIterator = dedupedBundleFiles.iterator();
-		while (bundleFileIterator.hasNext()) {
-			ResourceFile bundleFile = bundleFileIterator.next();
-			if (fileToBundleMap.containsKey(bundleFile)) {
-				bundleFileIterator.remove();
-				Msg.warn(this, "adding an already managed bundle: " + bundleFile.getAbsolutePath());
-			}
-		}
-		return dedupedBundleFiles;
-	}
-
 	/**
 	 * Create new GhidraBundles and add to the list of managed bundles.  All GhidraBundles created 
 	 * with the same {@code enabled} and {@code systemBundle} values. 
@@ -219,17 +203,8 @@ public class BundleHost {
 	 */
 	public Collection<GhidraBundle> add(List<ResourceFile> bundleFiles, boolean enabled,
 			boolean systemBundle) {
-		Set<ResourceFile> dedupedBundleFiles = dedupeBundleFiles(bundleFiles);
+		Collection<GhidraBundle> newBundles = bundleMap.computeAllIfAbsent(bundleFiles,
-		Map<ResourceFile, GhidraBundle> newBundleMap = dedupedBundleFiles.stream()
+			bundleFile -> createGhidraBundle(BundleHost.this, bundleFile, enabled, systemBundle));
-				.collect(Collectors.toUnmodifiableMap(Function.identity(),
-					bundleFile -> createGhidraBundle(BundleHost.this, bundleFile, enabled,
-						systemBundle)));
-		fileToBundleMap.putAll(newBundleMap);
-		bundleLocationToBundleMap.putAll(newBundleMap.values()
-				.stream()
-				.collect(Collectors.toUnmodifiableMap(GhidraBundle::getLocationIdentifier,
-					Function.identity())));
-		Collection<GhidraBundle> newBundles = newBundleMap.values();
 		fireBundlesAdded(newBundles);
 		return newBundles;
 	}
@@ -240,10 +215,7 @@ public class BundleHost {
 	 * @param bundles the bundles to add
 	 */
 	private void add(List<GhidraBundle> bundles) {
-		for (GhidraBundle bundle : bundles) {
+		bundleMap.addAll(bundles);
-			fileToBundleMap.put(bundle.getFile(), bundle);
-			bundleLocationToBundleMap.put(bundle.getLocationIdentifier(), bundle);
-		}
 		fireBundlesAdded(bundles);
 	}
 
@@ -253,8 +225,7 @@ public class BundleHost {
 	 * @param bundleFile the file of the bundle to remove
 	 */
 	public void remove(ResourceFile bundleFile) {
-		GhidraBundle bundle = fileToBundleMap.remove(bundleFile);
+		GhidraBundle bundle = bundleMap.remove(bundleFile);
-		bundleLocationToBundleMap.remove(bundle.getLocationIdentifier());
 		fireBundleRemoved(bundle);
 	}
 
@@ -264,8 +235,7 @@ public class BundleHost {
 	 * @param bundleLocation the location id of the bundle to remove
 	 */
 	public void remove(String bundleLocation) {
-		GhidraBundle bundle = bundleLocationToBundleMap.remove(bundleLocation);
+		GhidraBundle bundle = bundleMap.remove(bundleLocation);
-		fileToBundleMap.remove(bundle.getFile());
 		fireBundleRemoved(bundle);
 	}
 
@@ -275,8 +245,7 @@ public class BundleHost {
 	 * @param bundle the bundle to remove
 	 */
 	public void remove(GhidraBundle bundle) {
-		fileToBundleMap.remove(bundle.getFile());
+		bundleMap.remove(bundle);
-		bundleLocationToBundleMap.remove(bundle.getLocationIdentifier());
 		fireBundleRemoved(bundle);
 	}
 
@@ -286,10 +255,7 @@ public class BundleHost {
 	 * @param bundles the bundles to remove
 	 */
 	public void remove(Collection<GhidraBundle> bundles) {
-		for (GhidraBundle bundle : bundles) {
+		bundleMap.removeAll(bundles);
-			fileToBundleMap.remove(bundle.getFile());
-			bundleLocationToBundleMap.remove(bundle.getLocationIdentifier());
-		}
 		fireBundlesRemoved(bundles);
 	}
 
@@ -338,7 +304,7 @@ public class BundleHost {
 	 * @return all the bundles
 	 */
 	public Collection<GhidraBundle> getGhidraBundles() {
-		return fileToBundleMap.values();
+		return bundleMap.getGhidraBundles();
 	}
 
 	/**
@@ -347,7 +313,7 @@ public class BundleHost {
 	 * @return all the bundle files
 	 */
 	public Collection<ResourceFile> getBundleFiles() {
-		return fileToBundleMap.keySet();
+		return bundleMap.getBundleFiles();
 	}
 
 	void dumpLoadedBundles() {
@@ -861,7 +827,7 @@ public class BundleHost {
 			boolean isEnabled = bundleIsEnabled[i];
 			boolean isActive = bundleIsActive[i];
 			boolean isSystem = bundleIsSystem[i];
-			GhidraBundle bundle = fileToBundleMap.get(bundleFile);
+			GhidraBundle bundle = bundleMap.get(bundleFile);
 			if (bundle != null) {
 				if (isEnabled != bundle.isEnabled()) {
 					bundle.setEnabled(isEnabled);
@@ -900,14 +866,15 @@ public class BundleHost {
 	 * @param saveState the state object
 	 */
 	public void saveManagedBundleState(SaveState saveState) {
-		int numBundles = fileToBundleMap.size();
+		Collection<GhidraBundle> bundles = bundleMap.getGhidraBundles();
+		int numBundles = bundles.size();
 		String[] bundleFiles = new String[numBundles];
 		boolean[] bundleIsEnabled = new boolean[numBundles];
 		boolean[] bundleIsActive = new boolean[numBundles];
 		boolean[] bundleIsSystem = new boolean[numBundles];
 
 		int index = 0;
-		for (GhidraBundle bundle : fileToBundleMap.values()) {
+		for (GhidraBundle bundle : bundles) {
 			bundleFiles[index] = generic.util.Path.toPathString(bundle.getFile());
 			bundleIsEnabled[index] = bundle.isEnabled();
 			bundleIsActive[index] = bundle.isActive();
@@ -1081,7 +1048,7 @@ public class BundleHost {
 			GhidraBundle bundle;
 			switch (event.getType()) {
 				case BundleEvent.STARTED:
-					bundle = bundleLocationToBundleMap.get(osgiBundle.getLocation());
+					bundle = bundleMap.getBundleAtLocation(osgiBundle.getLocation());
 					if (bundle != null) {
 						fireBundleActivationChange(bundle, true);
 					}
@@ -1093,7 +1060,7 @@ public class BundleHost {
 					break;
 				// force "inactive" updates for all other states
 				default:
-					bundle = bundleLocationToBundleMap.get(osgiBundle.getLocation());
+					bundle = bundleMap.getBundleAtLocation(osgiBundle.getLocation());
 					if (bundle != null) {
 						fireBundleActivationChange(bundle, false);
 					}

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

@@ -0,0 +1,225 @@
+/* ###
+ * IP: GHIDRA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package ghidra.app.plugin.core.osgi;
+
+import java.util.*;
+import java.util.concurrent.locks.*;
+import java.util.function.Function;
+import java.util.stream.Collectors;
+
+import generic.jar.ResourceFile;
+
+/**
+ * A thread-safe container that maps {@link GhidraBundle}s by file and bundle location.
+ */
+public class BundleMap {
+	private final ReadWriteLock lock = new ReentrantReadWriteLock();
+	private final Lock readLock = lock.readLock();
+	private final Lock writeLock = lock.writeLock();
+
+	private final Map<ResourceFile, GhidraBundle> bundlesByFile = new HashMap<>();
+	private final Map<String, GhidraBundle> bundlesByLocation = new HashMap<>();
+
+	/**
+	 * Maps associations between a bundle, its file, and its bundle location.
+	 * 
+	 * @param bundle a GhidraBundle object
+	 */
+	public void add(GhidraBundle bundle) {
+		writeLock.lock();
+		try {
+			bundlesByFile.put(bundle.getFile(), bundle);
+			bundlesByLocation.put(bundle.getLocationIdentifier(), bundle);
+		}
+		finally {
+			lock.writeLock().unlock();
+		}
+	}
+
+	/**
+	 * Maps bundles in a collection.
+	 * 
+	 * <p>This is the same as calling {@link BundleMap#add(GhidraBundle)} for each bundle in {@code bundles}.
+	 * 
+	 * @param bundles a collection of GhidraBundle objects
+	 */
+	public void addAll(Collection<GhidraBundle> bundles) {
+		writeLock.lock();
+		try {
+			for (GhidraBundle bundle : bundles) {
+				bundlesByFile.put(bundle.getFile(), bundle);
+				bundlesByLocation.put(bundle.getLocationIdentifier(), bundle);
+			}
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Removes the mappings of a bundle. 
+	 * 
+	 * @param bundle a GhidraBundle object
+	 */
+	public void remove(GhidraBundle bundle) {
+		writeLock.lock();
+		try {
+			bundlesByFile.remove(bundle.getFile());
+			bundlesByLocation.remove(bundle.getLocationIdentifier());
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Removes all mappings of each bundle from a collection.
+	 * 
+	 * This is the same as calling {@link #remove(GhidraBundle)} for each bundle in {@code bundles}.
+	 * 
+	 * @param bundles a collection of GhidraBundle objects
+	 */
+	public void removeAll(Collection<GhidraBundle> bundles) {
+		writeLock.lock();
+		try {
+			for (GhidraBundle bundle : bundles) {
+				bundlesByFile.remove(bundle.getFile());
+				bundlesByLocation.remove(bundle.getLocationIdentifier());
+			}
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Removes the mapping for a bundle with a given bundle location.
+	 * 
+	 * @param bundleLocation a bundle location
+	 * @return the bundle removed
+	 */
+	public GhidraBundle remove(String bundleLocation) {
+		writeLock.lock();
+		try {
+			GhidraBundle bundle = bundlesByLocation.remove(bundleLocation);
+			bundlesByFile.remove(bundle.getFile());
+			return bundle;
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Removes the mapping for a bundle with a given file.
+	
+	 * @param bundleFile a bundle file
+	 * @return the bundle removed
+	 */
+	public GhidraBundle remove(ResourceFile bundleFile) {
+		writeLock.lock();
+		try {
+			GhidraBundle bundle = bundlesByFile.remove(bundleFile);
+			bundlesByLocation.remove(bundle.getLocationIdentifier());
+			return bundle;
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Creates and maps bundles from files in a collection that aren't already mapped.
+	 * 
+	 * @param bundleFiles a collection of bundle files
+	 * @param ctor a constructor for a GhidraBundle given a bundle file
+	 * @return the newly created GhidraBundle objects
+	 */
+	public Collection<GhidraBundle> computeAllIfAbsent(Collection<ResourceFile> bundleFiles,
+			Function<ResourceFile, GhidraBundle> ctor) {
+		writeLock.lock();
+		try {
+			Set<ResourceFile> newBundleFiles = new HashSet<>(bundleFiles);
+			newBundleFiles.removeAll(bundlesByFile.keySet());
+			List<GhidraBundle> newBundles =
+				newBundleFiles.stream().map(ctor).collect(Collectors.toList());
+			addAll(newBundles);
+			return newBundles;
+		}
+		finally {
+			writeLock.unlock();
+		}
+	}
+
+	/**
+	 * Returns the bundle with the given location.
+	 * 
+	 * @param location a bundle location
+	 * @return the bundle found or null
+	 */
+	public GhidraBundle getBundleAtLocation(String location) {
+		readLock.lock();
+		try {
+			return bundlesByLocation.get(location);
+		}
+		finally {
+			readLock.unlock();
+		}
+	}
+
+	/**
+	 * Returns the bundle with the given file.
+	 * 
+	 * @param bundleFile a bundle file
+	 * @return the bundle found or null
+	 */
+	public GhidraBundle get(ResourceFile bundleFile) {
+		readLock.lock();
+		try {
+			return bundlesByFile.get(bundleFile);
+		}
+		finally {
+			readLock.unlock();
+		}
+	}
+
+	/**
+	 * @return the currently mapped bundles
+	 */
+	public Collection<GhidraBundle> getGhidraBundles() {
+		readLock.lock();
+		try {
+			return new ArrayList<>(bundlesByFile.values());
+		}
+		finally {
+			readLock.unlock();
+		}
+	}
+
+	/**
+	 * @return the currently mapped bundle files
+	 */
+	public Collection<ResourceFile> getBundleFiles() {
+		readLock.lock();
+		try {
+			return new ArrayList<>(bundlesByFile.keySet());
+		}
+		finally {
+			readLock.unlock();
+		}
+	}
+
+}

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

@@ -133,4 +133,19 @@ public abstract class GhidraScriptProvider
 	protected void writeBody(PrintWriter writer) {
 		writer.println(getCommentCharacter() + "TODO Add User Code Here");
 	}
+
+	/**
+	 * Fixup a script name for searching in script directories.
+	 *
+	 * <p>This method is part of a poorly specified behavior that is due for future amendment, 
+	 * see {@link GhidraScriptUtil#fixupName(String)}.
+	 * 
+	 * @param scriptName the name of the script, must end with this provider's extension
+	 * @return a (relative) file path to the corresponding script
+	 */
+	@Deprecated
+	protected String fixupName(String scriptName) {
+		return scriptName;
+	}
+
 }

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

@@ -28,6 +28,7 @@ import generic.jar.ResourceFile;
 import ghidra.app.plugin.core.osgi.BundleHost;
 import ghidra.app.plugin.core.osgi.OSGiException;
 import ghidra.app.plugin.core.script.GhidraScriptMgrPlugin;
+import ghidra.app.util.headless.HeadlessAnalyzer;
 import ghidra.framework.Application;
 import ghidra.util.Msg;
 import ghidra.util.classfinder.ClassSearcher;
@@ -139,8 +140,7 @@ public class GhidraScriptUtil {
 		}
 		catch (IOException e) {
 			Msg.error(GhidraScriptUtil.class,
-				"Failed to find script in any script directory: " + sourceFile.toString(),
+				"Failed to find script in any script directory: " + sourceFile.toString(), e);
-				e);
 		}
 		return null;
 	}
@@ -293,14 +293,7 @@ public class GhidraScriptUtil {
 	 * @return the Ghidra script provider
 	 */
 	public static GhidraScriptProvider getProvider(ResourceFile scriptFile) {
-		String scriptFileName = scriptFile.getName().toLowerCase();
+		return findProvider(scriptFile.getName());
-
-		for (GhidraScriptProvider provider : getProviders()) {
-			if (scriptFileName.endsWith(provider.getExtension().toLowerCase())) {
-				return provider;
-			}
-		}
-		return null;
 	}
 
 	/**
@@ -310,13 +303,23 @@ public class GhidraScriptUtil {
 	 * @return true if a provider exists that can process the specified file
 	 */
 	public static boolean hasScriptProvider(ResourceFile scriptFile) {
-		String scriptFileName = scriptFile.getName().toLowerCase();
+		return findProvider(scriptFile.getName()) != null;
+	}
+
+	/**
+	 * Find the provider whose extension matches the given filename extension.
+	 * 
+	 * @param fileName name of script file
+	 * @return the first matching provider or null if no provider matches
+	 */
+	private static GhidraScriptProvider findProvider(String fileName) {
+		fileName = fileName.toLowerCase();
 		for (GhidraScriptProvider provider : getProviders()) {
-			if (scriptFileName.endsWith(provider.getExtension().toLowerCase())) {
+			if (fileName.endsWith(provider.getExtension().toLowerCase())) {
-				return true;
+				return provider;
 			}
 		}
-		return false;
+		return null;
 	}
 
 	/**
@@ -362,31 +365,35 @@ public class GhidraScriptUtil {
 	}
 
 	/**
-	 * Fixup name issues, such as package parts in the name and inner class names.
+	 * Fix script name issues for searching in script directories.
+	 * If no provider can be identified, Java is assumed.
 	 * 
-	 * <p>This method can handle names with or without '.java' at the end; names with 
+	 * <p>This method is part of a poorly specified behavior that is due for future amendment.
-	 * '$' (inner classes) and names with '.' characters for package separators
+	 * 
+	 * <p>It is used by {@link GhidraScript#runScript(String)} methods, 
+	 * {@link #createNewScript(String, String, ResourceFile, List)}, and by {@link HeadlessAnalyzer} for 
+	 * {@code preScript} and {@code postScript}.  The intent was to allow some freedom in how a user specifies
+	 * a script in two ways: 1) if the extension is omitted ".java" is assumed and 2) if a Java class name is
+	 * given it's converted to a relative path.
 	 *  
 	 * @param name the name of the script
-	 * @return the name as a '.java' file path (with '/'s and not '.'s)
+	 * @return the name as a file path
 	 */
+	@Deprecated
 	static String fixupName(String name) {
-		if (name.endsWith(".java")) {
+		GhidraScriptProvider provider = findProvider(name);
-			name = name.substring(0, name.length() - 5);
+		// assume Java if no provider matched
+		if (provider == null) {
+			name = name + ".java";
+			provider = findProvider(".java");
 		}
-
+		return provider.fixupName(name);
-		String path = name.replace('.', '/');
-		int innerClassIndex = path.indexOf('$');
-		if (innerClassIndex != -1) {
-			path = path.substring(0, innerClassIndex);
-		}
-		return path + ".java";
 	}
 
 	static ResourceFile findScriptFileInPaths(Collection<ResourceFile> scriptDirectories,
-			String filename) {
+			String name) {
 
-		String validatedName = fixupName(filename);
+		String validatedName = fixupName(name);
 
 		for (ResourceFile resourceFile : scriptDirectories) {
 			if (resourceFile.isDirectory()) {

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

@@ -164,4 +164,29 @@ public class JavaScriptProvider extends GhidraScriptProvider {
 		return "//";
 	}
 
+	/**
+	 *
+	 * Fix script name for search in script directories, such as Java package parts in the name and inner class names.
+	 *
+	 * <p>This method can handle names with '$' (inner classes) and names with '.' 
+	 * characters for package separators
+	 *
+	 * <p>It is part of a poorly specified behavior that is due for future amendment, 
+	 * see {@link GhidraScriptUtil#fixupName(String)}.
+	 *
+	 * @param scriptName the name of the script
+	 * @return the name as a '.java' file path (with '/'s and not '.'s)
+	 */
+	@Override
+	protected String fixupName(String scriptName) {
+		scriptName = scriptName.substring(0, scriptName.length() - 5);
+
+		String path = scriptName.replace('.', '/');
+		int innerClassIndex = path.indexOf('$');
+		if (innerClassIndex != -1) {
+			path = path.substring(0, innerClassIndex);
+		}
+		return path + ".java";
+	}
+
 }

Ghidra/Features/Base/src/test.slow/java/ghidra/app/merge/datatypes/DataTypeMerge3Test.java

@@ -17,8 +17,7 @@ package ghidra.app.merge.datatypes;
 
 import static org.junit.Assert.*;
 
-import org.junit.Assert;
+import org.junit.*;
-import org.junit.Test;
 
 import ghidra.program.database.*;
 import ghidra.program.model.data.*;
@@ -1247,6 +1246,122 @@ public class DataTypeMerge3Test extends AbstractDataTypeMergeTest {
 
 	}
 
+	@Test
+	@Ignore
+	public void testEditStructureWithReplacementAndRemoval() throws Exception {
+
+		// See GP-585 for design issue preventing this test from passing
+
+		mtf.initialize("notepad", new OriginalProgramModifierListener() {
+
+			@Override
+			public void modifyPrivate(ProgramDB program) throws Exception {
+				boolean commit = false;
+				DataTypeManager dtm = program.getDataTypeManager();
+				int transactionID = program.startTransaction("test");
+				try {
+					Structure s = (Structure) dtm.getDataType("/Category5/Test");
+					DataType dt = dtm.getDataType("/MISC/FooTypedef");
+					s.setFlexibleArrayComponent(dt, "foo", "");
+					commit = true;
+				}
+				finally {
+					program.endTransaction(transactionID, commit);
+				}
+			}
+
+			@Override
+			public void modifyLatest(ProgramDB program) throws Exception {
+				boolean commit = false;
+				DataTypeManager dtm = program.getDataTypeManager();
+				int transactionID = program.startTransaction("test");
+				try {
+					TypeDef td = (TypeDef) dtm.getDataType("/BF");
+					//
+					// NOTE: Merge does not handle datatype replacements as one might hope
+					// If latest version has defined data/components based upon a type which has
+					// been replaced in private, the replaced datatype will be treated as removed
+					//
+					dtm.replaceDataType(td, new TypedefDataType("NewBF", IntegerDataType.dataType),
+						true);
+					DataType dt = dtm.getDataType("/MISC/FooTypedef");
+					dtm.remove(dt, TaskMonitor.DUMMY);
+					commit = true;
+				}
+				finally {
+					program.endTransaction(transactionID, commit);
+				}
+
+				DataType dt1 = dtm.getDataType("/BF");
+				assertNull(dt1);
+			}
+
+			@Override
+			public void modifyOriginal(ProgramDB program) throws Exception {
+				boolean commit = false;
+				DataTypeManager dtm = program.getDataTypeManager();
+				int transactionID = program.startTransaction("test");
+				try {
+					TypeDef td = new TypedefDataType("BF", IntegerDataType.dataType);
+
+					Structure struct = new StructureDataType(new CategoryPath("/Category5"), "Test",
+						0, program.getDataTypeManager());
+					struct.add(td);
+					struct.insertBitFieldAt(3, 2, 6, td, 2, "bf1", null);
+					struct.insertBitFieldAt(3, 2, 4, td, 2, "bf2", null);
+					struct.add(new WordDataType());
+					struct.add(new QWordDataType());
+
+					struct.setFlexibleArrayComponent(td, "flex", "my flex");
+
+					dtm.addDataType(struct, null);
+					commit = true;
+				}
+				catch (Exception e) {
+					e.printStackTrace();
+					Assert.fail(e.toString());
+				}
+				finally {
+					program.endTransaction(transactionID, commit);
+				}
+			}
+		});
+
+		executeMerge(DataTypeMergeManager.OPTION_MY);
+
+		DataTypeManager dtm = resultProgram.getDataTypeManager();
+
+		DataType dt = dtm.getDataType("/Category5/Test");
+		assertTrue(dt instanceof Structure);
+		Structure s = (Structure) dt;
+		/** Current Result for /Category5/Test
+		 * 
+				Unaligned
+				Structure Test {
+				   4   int:2(6)   1   bf1   ""
+				   4   int:2(4)   1   bf2   ""
+				   5   word   2   null   ""
+				   7   qword   8   null   ""
+				}
+				Size = 15   Actual Alignment = 1
+		 *	
+		 * See assertion below for preferred result
+		 */
+		//@formatter:off
+		assertEquals("/Category5/Test\n" + 
+			"Unaligned\n" + 
+			"Structure Test {\n" + 
+			"   0   NewBF   4   null   \"\"\n" + 
+			"   4   NewBF:2(6)   1   bf1   \"\"\n" + 
+			"   4   NewBF:2(4)   1   bf2   \"\"\n" + 
+			"   5   word   2   null   \"\"\n" + 
+			"   7   qword   8   null   \"\"\n" + 
+			"   Undefined1[0]   0   foo   \"\"\n" +  // reflects removal of /MISC/FooTypedef
+			"}\n" + 
+			"Size = 15   Actual Alignment = 1\n", s.toString());
+		//@formatter:on
+	}
+
 	@Test
 	public void testEditUnions() throws Exception {
 

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

@@ -669,6 +669,8 @@ public class DefaultGraphDisplay implements GraphDisplay {
 		// always get the current predicate from the main view and test with it,
 		satellite.getRenderContext()
 				.setVertexIncludePredicate(v -> viewer.getRenderContext().getVertexIncludePredicate().test(v));
+		satellite.getRenderContext()
+				.setEdgeIncludePredicate(e -> viewer.getRenderContext().getEdgeIncludePredicate().test(e));
 		satellite.getComponent().setBorder(BorderFactory.createEtchedBorder());
 		parentViewer.getComponent().addComponentListener(new ComponentAdapter() {
 			@Override

Ghidra/Framework/SoftwareModeling/src/main/java/ghidra/program/database/data/DataTypeManagerDB.java

@@ -1473,11 +1473,12 @@ abstract public class DataTypeManagerDB implements DataTypeManager {
 	public DataType getDataType(String dataTypePath) {
 		// Category path now has sourceID followed by ":" followed by path under that source.
 		String name = getName();
-		if (dataTypePath.startsWith(name)) {
+		int nameLen = name.length();
-			dataTypePath = dataTypePath.substring(name.length());
+		if (dataTypePath.length() > nameLen && dataTypePath.charAt(nameLen) == '/' &&
+			dataTypePath.startsWith(name)) {
+			dataTypePath = dataTypePath.substring(nameLen);
 		}
-
+		else if (!dataTypePath.startsWith("/")) {
-		if (!dataTypePath.startsWith("/")) {
 			return null;
 		}
 

Ghidra/RuntimeScripts/Windows/support/createPdbXmlFiles.bat

@@ -26,7 +26,7 @@ set OS_DIR=build\os
 :continue
 
 REM create absolute path
-for /f %%i in ("%GHIDRA_DIR%") do set GHIDRA_DIR=%%~fi
+for /f "delims=" %%i in ("%GHIDRA_DIR%") do set GHIDRA_DIR=%%~fi
 
 REM Determine if 64-bit or 32-bit
 if exist "%PROGRAMFILES(X86)%" (
@@ -64,7 +64,7 @@ for /f "tokens=* delims=" %%a in ('dir %arg1% /s /b') do (
 			setlocal enableDelayedExpansion
 			(
 				echo "Processing file: %%a"
-				START /B /WAIT "" "%PDB_EXE%" %%a > "%%a.xml"
+				START /B /WAIT "" "%PDB_EXE%" "%%a" > "%%a.xml"
 
 				REM Exit if executable returned non-zero error code (signifies that there is a problem).
 				if !errorlevel! neq 0 (

Ghidra/Test/IntegrationTest/src/test.slow/java/ghidra/app/script/GhidraScriptUtilTest.java

@@ -15,14 +15,23 @@
  */
 package ghidra.app.script;
 
-import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.*;
 
+import org.junit.Before;
 import org.junit.Test;
 
 import generic.test.AbstractGenericTest;
+import ghidra.util.classfinder.ClassSearcher;
+import ghidra.util.exception.CancelledException;
+import ghidra.util.task.ConsoleTaskMonitor;
 
 public class GhidraScriptUtilTest extends AbstractGenericTest {
 
+	@Before
+	public void setup() throws CancelledException {
+		ClassSearcher.search(false, new ConsoleTaskMonitor());
+	}
+
 	@Test
 	public void fixupName_WithExtension() {
 		String input = "Bob.java";
@@ -58,4 +67,11 @@ public class GhidraScriptUtilTest extends AbstractGenericTest {
 		String input = "a.b.c.Bob$InnerClass";
 		assertEquals(GhidraScriptUtil.fixupName(input), "a/b/c/Bob.java");
 	}
+
+	@Test
+	public void fixupName_Python() {
+		String input = "Bob.py";
+		assertEquals(GhidraScriptUtil.fixupName(input), "Bob.py");
+	}
+
 }