GP-2509 GP-2644 Improved Ghidra URL support. Added support for Ghidra

URL linked files and folders within project.

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

@@ -27,6 +27,7 @@ import ghidra.framework.data.ProjectFileManager;
 import ghidra.framework.model.*;
 import ghidra.framework.options.SaveState;
 import ghidra.framework.plugintool.PluginTool;
+import ghidra.framework.store.LockException;
 import ghidra.trace.database.DBTraceContentHandler;
 import ghidra.trace.model.Lifespan;
 import ghidra.trace.model.Trace;
@@ -643,6 +644,7 @@ public class DebuggerCoordinates {
 		ProjectData projData = tool.getProject().getProjectData(projLoc);
 		if (projData == null) {
 			try {
+				// FIXME! orphaned instance - transient in nature
 				projData = new ProjectFileManager(projLoc, false, false);
 			}
 			catch (NotOwnerException e) {
@@ -650,7 +652,7 @@ public class DebuggerCoordinates {
 					"Not project owner: " + projLoc + "(" + pathname + ")");
 				return null;
 			}
-			catch (IOException e) {
+			catch (IOException | LockException e) {
 				Msg.showError(DebuggerCoordinates.class, tool.getToolFrame(), "Trace Open Failed",
 					"Project error: " + e.getMessage());
 				return null;

Ghidra/Debug/Debugger/src/main/java/ghidra/app/plugin/core/debug/service/tracemgr/DebuggerTraceManagerServicePlugin.java

@@ -368,7 +368,18 @@ public class DebuggerTraceManagerServicePlugin extends Plugin
 		if (traceChooserDialog != null) {
 			return traceChooserDialog;
 		}
-		DomainFileFilter filter = df -> Trace.class.isAssignableFrom(df.getDomainObjectClass());
+		DomainFileFilter filter = new DomainFileFilter() {
+
+			@Override
+			public boolean accept(DomainFile df) {
+				return Trace.class.isAssignableFrom(df.getDomainObjectClass());
+			}
+
+			@Override
+			public boolean followLinkedFolders() {
+				return false;
+			}
+		};
 
 		// TODO regarding the hack note below, I believe this issue ahs been fixed, but not sure how to test
 		return traceChooserDialog =

Ghidra/Debug/Debugger/src/test/java/ghidra/app/plugin/core/debug/service/url/ProjectExperimentsTest.java

@@ -176,7 +176,7 @@ public class ProjectExperimentsTest extends AbstractGhidraHeadedIntegrationTest
 
 		assertNotNull(proj2 = pm.openProject(loc2, false, false));
 
-		ProjectData data1 = proj2.addProjectView(loc1.getURL());
+		ProjectData data1 = proj2.addProjectView(loc1.getURL(), true);
 		assertNotNull(data1);
 
 		// It's a cryin' shame. I don't get *any* callbacks. _ANY!_

Ghidra/Debug/Framework-TraceModeling/src/main/java/ghidra/trace/database/DBTraceContentHandler.java

@@ -18,11 +18,13 @@ package ghidra.trace.database;
 import java.io.IOException;
 
 import javax.swing.Icon;
+import javax.swing.ImageIcon;
 
 import db.DBHandle;
 import db.buffers.BufferFile;
 import db.buffers.ManagedBufferFile;
-import ghidra.framework.data.*;
+import ghidra.framework.data.DBWithUserDataContentHandler;
+import ghidra.framework.data.DomainObjectMergeManager;
 import ghidra.framework.model.ChangeSet;
 import ghidra.framework.model.DomainObject;
 import ghidra.framework.store.*;
@@ -34,9 +36,16 @@ import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.VersionException;
 import ghidra.util.task.TaskMonitor;
 
-public class DBTraceContentHandler extends DBContentHandler {
+public class DBTraceContentHandler extends DBWithUserDataContentHandler<DBTrace> {
 	public static final String TRACE_CONTENT_TYPE = "Trace";
 
+	public static ImageIcon TRACE_ICON = Trace.TRACE_ICON;
+
+	static final Class<DBTrace> TRACE_DOMAIN_OBJECT_CLASS = DBTrace.class;
+	static final String TRACE_CONTENT_DEFAULT_TOOL = "Debugger";
+
+	private static final DBTraceLinkContentHandler linkHandler = new DBTraceLinkContentHandler();
+
 	@Override
 	public long createFile(FileSystem fs, FileSystem userfs, String path, String name,
 			DomainObject obj, TaskMonitor monitor)
@@ -48,7 +57,7 @@ public class DBTraceContentHandler extends DBContentHandler {
 	}
 
 	@Override
-	public DomainObjectAdapter getImmutableObject(FolderItem item, Object consumer, int version,
+	public DBTrace getImmutableObject(FolderItem item, Object consumer, int version,
 			int minChangeVersion, TaskMonitor monitor)
 			throws IOException, CancelledException, VersionException {
 		String contentType = item.getContentType();
@@ -96,7 +105,7 @@ public class DBTraceContentHandler extends DBContentHandler {
 	}
 
 	@Override
-	public DomainObjectAdapter getReadOnlyObject(FolderItem item, int version, boolean okToUpgrade,
+	public DBTrace getReadOnlyObject(FolderItem item, int version, boolean okToUpgrade,
 			Object consumer, TaskMonitor monitor)
 			throws IOException, VersionException, CancelledException {
 		String contentType = item.getContentType();
@@ -146,7 +155,7 @@ public class DBTraceContentHandler extends DBContentHandler {
 	}
 
 	@Override
-	public DomainObjectAdapter getDomainObject(FolderItem item, FileSystem userfs, long checkoutId,
+	public DBTrace getDomainObject(FolderItem item, FileSystem userfs, long checkoutId,
 			boolean okToUpgrade, boolean recover, Object consumer, TaskMonitor monitor)
 			throws IOException, CancelledException, VersionException {
 		String contentType = item.getContentType();
@@ -296,8 +305,8 @@ public class DBTraceContentHandler extends DBContentHandler {
 	}
 
 	@Override
-	public Class<? extends DomainObject> getDomainObjectClass() {
+	public Class<DBTrace> getDomainObjectClass() {
-		return DBTrace.class;
+		return TRACE_DOMAIN_OBJECT_CLASS;
 	}
 
 	@Override
@@ -312,12 +321,12 @@ public class DBTraceContentHandler extends DBContentHandler {
 
 	@Override
 	public String getDefaultToolName() {
-		return "Debugger";
+		return TRACE_CONTENT_DEFAULT_TOOL;
 	}
 
 	@Override
 	public Icon getIcon() {
-		return Trace.TRACE_ICON;
+		return TRACE_ICON;
 	}
 
 	@Override
@@ -331,4 +340,9 @@ public class DBTraceContentHandler extends DBContentHandler {
 		// TODO:
 		return null;
 	}
+
+	@Override
+	public DBTraceLinkContentHandler getLinkHandler() {
+		return linkHandler;
+	}
 }

Ghidra/Debug/Framework-TraceModeling/src/main/java/ghidra/trace/database/DBTraceLinkContentHandler.java

@@ -0,0 +1,71 @@
+/* ###
+ * 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.trace.database;
+
+import java.io.IOException;
+
+import javax.swing.Icon;
+
+import ghidra.framework.data.LinkHandler;
+import ghidra.framework.data.URLLinkObject;
+import ghidra.framework.model.DomainObject;
+import ghidra.framework.store.FileSystem;
+import ghidra.util.InvalidNameException;
+import ghidra.util.exception.CancelledException;
+import ghidra.util.task.TaskMonitor;
+
+public class DBTraceLinkContentHandler extends LinkHandler<DBTrace> {
+
+	public static final String TRACE_LINK_CONTENT_TYPE = "TraceLink";
+
+	@Override
+	public long createFile(FileSystem fs, FileSystem userfs, String path, String name,
+			DomainObject obj, TaskMonitor monitor)
+			throws IOException, InvalidNameException, CancelledException {
+		if (!(obj instanceof URLLinkObject)) {
+			throw new IOException("Unsupported domain object: " + obj.getClass().getName());
+		}
+		return createFile((URLLinkObject) obj, TRACE_LINK_CONTENT_TYPE, fs, path, name,
+			monitor);
+	}
+
+	@Override
+	public String getContentType() {
+		return TRACE_LINK_CONTENT_TYPE;
+	}
+
+	@Override
+	public String getContentTypeDisplayString() {
+		return TRACE_LINK_CONTENT_TYPE;
+	}
+
+	@Override
+	public Class<DBTrace> getDomainObjectClass() {
+		// return linked content class
+		return DBTraceContentHandler.TRACE_DOMAIN_OBJECT_CLASS;
+	}
+
+	@Override
+	public Icon getIcon() {
+		return DBTraceContentHandler.TRACE_ICON;
+	}
+
+	@Override
+	public String getDefaultToolName() {
+		return DBTraceContentHandler.TRACE_CONTENT_DEFAULT_TOOL;
+	}
+
+}

Ghidra/Features/Base/certification.manifest

@@ -351,6 +351,7 @@ src/main/help/help/topics/FrontEndPlugin/images/DeleteProject.png||GHIDRA||||END
 src/main/help/help/topics/FrontEndPlugin/images/EditPluginPath.png||GHIDRA||||END|
 src/main/help/help/topics/FrontEndPlugin/images/EditProjectAccessList.png||GHIDRA||||END|
 src/main/help/help/topics/FrontEndPlugin/images/EditProjectAccessPanel.png||GHIDRA||||END|
+src/main/help/help/topics/FrontEndPlugin/images/LinkOtherProject.png||GHIDRA||||END|
 src/main/help/help/topics/FrontEndPlugin/images/MemoryUsage.png||GHIDRA||||END|
 src/main/help/help/topics/FrontEndPlugin/images/NonSharedProjectInfo.png||GHIDRA||||END|
 src/main/help/help/topics/FrontEndPlugin/images/OpenProject.png||GHIDRA||||END|
@@ -1089,7 +1090,6 @@ src/main/resources/images/layout_add.png||FAMFAMFAM Icons - CC 2.5|||famfamfam s
 src/main/resources/images/ledgreen.png||Nuvola Icons - LGPL 2.1|||Nuvola icon set|END|
 src/main/resources/images/ledred.png||Nuvola Icons - LGPL 2.1|||Nuvola icon set|END|
 src/main/resources/images/ledyellow.png||Nuvola Icons - LGPL 2.1|||Nuvola icon set|END|
-src/main/resources/images/link.png||Nuvola Icons - LGPL 2.1|||Nuvola icon set|END|
 src/main/resources/images/lock.gif||GHIDRA||||END|
 src/main/resources/images/magnifier.png||FAMFAMFAM Icons - CC 2.5||||END|
 src/main/resources/images/media-flash.png||Oxygen Icons - LGPL 3.0|||Oxygen icon theme (dual license; LGPL or CC-SA-3.0)|END|

Ghidra/Features/Base/ghidra_scripts/CallAnotherScriptForAllPrograms.java

@@ -17,6 +17,8 @@
 // NOTE: Script will only process unversioned and checked-out files.
 //@category Examples
 
+import java.io.IOException;
+
 import ghidra.app.script.GhidraScript;
 import ghidra.app.script.GhidraState;
 import ghidra.framework.model.*;
@@ -25,8 +27,6 @@ import ghidra.program.model.listing.Program;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.VersionException;
 
-import java.io.IOException;
-
 public class CallAnotherScriptForAllPrograms extends GhidraScript {
 
 	// The script referenced in the following line should be replaced with the script to be called
@@ -59,6 +59,10 @@ public class CallAnotherScriptForAllPrograms extends GhidraScript {
 	}
 
 	private void processDomainFile(DomainFile domainFile) throws CancelledException, IOException {
+		// Do not follow folder-links or consider program links.  Using content type
+		// to filter is best way to control this.  If program links should be considered
+		// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+		// should be used.
 		if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domainFile.getContentType())) {
 			return; // skip non-Program files
 		}

Ghidra/Features/Base/ghidra_scripts/RepositoryFileUpgradeScript.java

@@ -143,6 +143,8 @@ public class RepositoryFileUpgradeScript extends GhidraScript {
 	}
 
 	private boolean performProgramUpgrade(DomainFile df) throws IOException, CancelledException {
+		// Do not follow folder-links or consider program links.  Using content type
+		// to filter is best way to control this.
 		if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(df.getContentType())) {
 			return false;
 		}

Ghidra/Features/Base/ghidra_scripts/VersionControl_AddAll.java

@@ -48,7 +48,10 @@ public class VersionControl_AddAll extends GhidraScript {
 			if (monitor.isCancelled()) {
 				break;
 			}
-
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.  It may also be appropriate to handle other content types.
 			if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(file.getContentType()) ||
 				file.isVersioned()) {
 				continue;// skip

Ghidra/Features/Base/src/main/help/help/topics/Annotations/Annotations.html

@@ -22,13 +22,15 @@
     hyperlink.</P>
     <!-- Annotation Example -->
 
-    <P>The following text shows the syntax of the URL annotation:</P>
+    <P>The following text shows the syntax of a sample URL annotation:</P>
 	<pre><font size="4"><br>
-	<b>{@<i>url</i></b> "http://www.google.com"<b>}</b><br>
+	<b>{@<i>url</i></b> "<i>http://www.google.com</i>"</b> "Search Web"<b>}</b><br>
 	</font><br></pre>
 
     <P>The bold text is required for all annotations. The italicized text is required but is
-    specific to the annotation being used (see the table below).</P>
+    specific to the annotation being used (see the table below).  The optional rendered display text
+    "Search Web" will be displayed in listing.  If the optional display test is omitted, the URL 
+    will be displayed.  Quotes around display text are optional.</P>
 
     <H2>Examples</H2>
 
@@ -47,10 +49,21 @@
        <I>Rendered URL Annotation Example</I></P>
 
       <P>When the URL text (e.g., "http://www.google.com") in the above image is clicked from within
-      Ghidra, a web browser is launched and attempts to load the corresponding web page.  If the URL text
+      Ghidra, a web browser is launched and attempts to load the corresponding web page.  </P>
-      is of the form <i>ghidra://&lt;host&gt;[:&lt;port&gt;]/&lt;repository-name&gt;/&lt;program-path&gt;[#&lt;address-or-symbol-ref&gt;]</i>
+      
-      an attempt will be made to open the corresponding program from the referenced Ghidra Server (e.g., 
+      <P>If the URL text corresponds to a Ghidra URL and attempt will be made to open the referenced
-      <i>ghidra://myserver/Repo/notepad.exe#entry</i>).</P>
+      Program file within the Code Browser.  Such a URL may refer to a Program file from a 
+      local project or Ghidra Server.  The Ghidra URL forms supported include:</P>
+      
+      <P><U>Remote Ghidra Server file</U><BR>
+      <i>ghidra://&lt;host&gt;[:&lt;port&gt;]/&lt;repository-name&gt;/&lt;program-path&gt;[#&lt;address-or-symbol-ref&gt;]</i><BR>
+      Example: <i>ghidra://hostname/Repo/notepad.exe#entry</i>
+      </P>
+      
+      <P><U>Local Ghidra project file</U><BR>
+      <i>ghidra:/[&lt;project-path&gt/]&lt;project-name&gt;?/&lt;program-path&gt;[#&lt;address-or-symbol-ref&gt;]</i><BR>
+      Example: <i>ghidra:/share/MyProject?/notepad.exe#entry</i>
+      </P>
     </BLOCKQUOTE>
 
     <H2>Valid Annotations</H2>
@@ -174,9 +187,10 @@
             <TD valign="top" width="15%">Displays the given URL has a hyperlink. This annotation
             optionally takes display text so that the hyperlink may be displayed with text other
             than that of the URL.<BR><BR>
-            References to <i>ghidra://</i>, which refer to a program within a Ghidra Server repository,
+            References to a program file on a Ghidra Server (<i>ghidra://&lt;host...</i>) or 
-            will be opened within the Listing display, while all other URL protocols (e.g., <i>http://, https://,
+            local project (<i>ghidra:/&lt;project-...</i>) will be opened within the Listing display, 
-            file://,</i> etc.) will be launched via an external web browser (see 
+            while all other URL forms (e.g., <i>http://, https://, file://,</i> etc.) will be 
+            launched via an external web browser (see 
             <a href="help/topics/ShowInstructionInfoPlugin/ShowInstructionInfo.htm#Show_Processor_Manual">command configuration 
             for Processor Manuals</a>). 
             </TD>
@@ -216,6 +230,12 @@
                 <LI>{@url "ghidra://myserver/Repo/notepad.exe#entry"}</LI>
                 
                 <LI>{@url "ghidra://myserver/Repo/notepad.exe" "see notepad.exe"}</LI>
+                
+                <LI>{@url "ghidra:/share/MyProject?/notepad.exe#entry"}</LI>
+                
+                <LI>{@url "ghidra:/share/MyProject?/notepad.exe" "see notepad.exe"}</LI>
+                
+                
               </UL>
             </TD>
           </TR>
@@ -224,8 +244,9 @@
             <TD valign="top" width="5%">Program<BR>
             </TD>
 
-            <TD valign="top" width="15%">Displays a hyperlink to the given Ghidra program name that
+            <TD valign="top" width="15%">Displays a hyperlink to the given Ghidra program pathname 
-            will open that program in a new Listing tab when clicked.<BR>
+            with the current project.  Referenced program 
+            will open in a new Listing tab when clicked.<BR>
              You may optionally provide an address or symbol to be displayed when the program is
             opened by appending to the program name an '@' character, followed by an address or
             symbol name.</TD>

Ghidra/Features/Base/src/main/help/help/topics/FrontEndPlugin/Ghidra_Front_end.htm

@@ -688,6 +688,54 @@
 
         <P>The tabbed pane for read-only Project data is removed from the Project Window.</P>
       </BLOCKQUOTE>
+      
+      <H3><A name="Create_File_Links"></A>Create Linked Folder or File</H3>
+      
+      <BLOCKQUOTE>
+        <P>This feature allows you to create a folder or file link in your active project to a 
+        corresponding folder or file within a read-only viewed project.  
+        This is done using a Ghidra URL which references the 
+        file in its local or remote storage location.  If the viewed project corresponds to a 
+        viewed repository a remote URL will be used, while other cases will refer to the
+        locally viewed project.  It is possible for links to become broken if the referenced
+        repository, local project or file location are changed.</P>
+        <ol>
+        <li>Select a single folder or file from a viewed READ-ONLY Project Data tree.</li>
+        <li>Right mouse click on the selected tree node and choose the <I>Copy</I> option.</li>
+        <li>Select a destination folder in the active project tree.</li>
+        <li>Right mouse click on the folder and choose the <I>Paste as Link</I> option.
+            <P><IMG src="../../shared/note.png" border="0">Currently, linked-file types are 
+            currently limited to <I>Program</I> and <I>Data Type Archive</I> files 
+            only.  The <I>Past as Link</I> menu item will be disabled for 
+            unsupported file content types or for other unsupported situations such as internal 
+            linking within the same project.</P>
+            </li>
+        </ol>
+        <P>A linked-file may be opened in a tool via the project window in the same fashion that 
+        a normal file is opened (e.g., double-left-mouse-click or drag-n-drop onto a tool box icon).
+        Such a project file may also be opened within a Tool using its <B>File->Open...</B> action
+        and selected from the resulting project file selection dilaog.
+        Clicking on a linked-folder in the active project window will open that location in a
+        <B>READ-ONLY Project Data</B> tree.  The user may be prompted for a shared repository
+        connection password when accessing a linked folder or file.</P>
+        <P>Within a project file chooser dialog a linked-folder may be expanded in a similar fashion
+        to local folders provided any neccessary repository connection can be completed.</P>
+        <P><IMG src="../../shared/note.png" border="0"><B>Add to Version Control...</B> is supported
+        for repository folder and file links only and will be disabled for links to a 
+        local project.</P>
+        <P><IMG src="../../shared/note.png" border="0">Currently, linked-files only provide access
+        to the latest file version and do not facilitate access to older file versions.</P>
+        <P>The project window below shows a Program file-link "Program1" which is linked to the
+        same file in the viewed project.  Hovering the mouse over a linked-file will show the URL 
+        of the linked file or folder.  The chain-link icon decoration indicates such a linked 
+        file or folder.</P>
+        
+        <CENTER>
+          <IMG src= "images/LinkOtherProject.png" border="0">
+        </CENTER>
+        
+      </BLOCKQUOTE>
+      
     </BLOCKQUOTE>
 
     <H2><A name="Workspace"></A>Workspaces</H2>

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/calltree/CallTreeProvider.java

@@ -1266,19 +1266,24 @@ public class CallTreeProvider extends ComponentProviderAdapter implements Domain
 		}
 
 		@Override
-		protected void expandNode(GTreeNode node, TaskMonitor monitor) throws CancelledException {
+		protected void expandNode(GTreeNode node, boolean force, TaskMonitor monitor)
+				throws CancelledException {
 			TreePath treePath = node.getTreePath();
 			Object[] path = treePath.getPath();
 			if (path.length > maxDepth) {
 				return;
 			}
 
+			if (!force && !node.isAutoExpandPermitted()) {
+				return;
+			}
+
 			CallNode callNode = (CallNode) node;
 			if (callNode.functionIsInPath()) {
 				return; // this path hit a function that is already in the path
 			}
 
-			super.expandNode(node, monitor);
+			super.expandNode(node, false, monitor);
 		}
 	}
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/clear/ClearFlowAndRepairCmd.java

@@ -106,9 +106,33 @@ public class ClearFlowAndRepairCmd extends BackgroundCommand {
 				CodeUnit cu = cuIter.next();
 				if (cu instanceof Instruction) {
 					Instruction instr = (Instruction) cu;
+
+					// check for function on delay slot
+					if (listing.getFunctionAt(instr.getMinAddress()) != null) {
+						continue; // skip since it will be picked-up by flow if appropriate
+					}
+
+					// check for fallthrough to instruction
 					Address ffAddr = instr.getFallFrom();
 					if (ffAddr != null && startAddrs.contains(ffAddr)) {
-						continue; // skip since it will be picked-up by flow
+						continue; // skip since it will be picked-up by flow if appropriate
+					}
+
+					// check for flow into delay slot
+					if (instr.isInDelaySlot()) {
+						boolean skip = false;
+						ReferenceIterator refToIter = instr.getReferenceIteratorTo();
+						while (refToIter.hasNext()) {
+							Reference ref = refToIter.next();
+							RefType refType = ref.getReferenceType();
+							if (refType.isJump() || refType.isCall()) {
+								skip = true;
+								break;
+							}
+						}
+						if (skip) {
+							continue; // skip since it will be picked-up by flow if appropriate
+						}
 					}
 				}
 				else {

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/comments/CommentsDialog.java

@@ -240,10 +240,11 @@ public class CommentsDialog extends DialogComponentProvider implements KeyListen
 	////////////////////////////////////////////////////////////////////
 
 	private AnnotationAdapterWrapper[] getAnnotationAdapterWrappers() {
-		AnnotatedStringHandler[] annotations = Annotation.getAnnotatedStringHandlers();
+		List<AnnotatedStringHandler> annotations = Annotation.getAnnotatedStringHandlers();
-		AnnotationAdapterWrapper[] retVal = new AnnotationAdapterWrapper[annotations.length];
+		int count = annotations.size();
-		for (int i = 0; i < annotations.length; i++) {
+		AnnotationAdapterWrapper[] retVal = new AnnotationAdapterWrapper[count];
-			retVal[i] = new AnnotationAdapterWrapper(annotations[i]);
+		for (int i = 0; i < count; i++) {
+			retVal[i] = new AnnotationAdapterWrapper(annotations.get(i));
 		}
 		return retVal;
 	}

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/datamgr/DataTypeManagerPlugin.java

@@ -56,7 +56,6 @@ import ghidra.framework.options.SaveState;
 import ghidra.framework.plugintool.PluginInfo;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.framework.plugintool.util.PluginStatus;
-import ghidra.program.database.DataTypeArchiveContentHandler;
 import ghidra.program.database.data.ProgramDataTypeManager;
 import ghidra.program.model.address.AddressSetView;
 import ghidra.program.model.data.*;
@@ -245,8 +244,7 @@ public class DataTypeManagerPlugin extends ProgramPlugin
 		Project project = tool.getProjectManager().getActiveProject();
 		if (project != null && project.getName().equals(projectName)) {
 			DomainFile df = project.getProjectData().getFile(pathname);
-			if (df != null && DataTypeArchiveContentHandler.DATA_TYPE_ARCHIVE_CONTENT_TYPE
+			if (DataTypeArchive.class.isAssignableFrom(df.getDomainObjectClass())) {
-					.equals(df.getContentType())) {
 				return df;
 			}
 		}
@@ -588,12 +586,9 @@ public class DataTypeManagerPlugin extends ProgramPlugin
 					openArchive(domainFile, version);
 				}
 			};
-			DomainFileFilter filter = f -> {
-				Class<?> c = f.getDomainObjectClass();
-				return DataTypeArchive.class.isAssignableFrom(c);
-			};
 			openDialog =
-				new OpenVersionedFileDialog(tool, "Open Project Data Type Archive", filter);
+				new OpenVersionedFileDialog(tool, "Open Project Data Type Archive",
+					df -> DataTypeArchive.class.isAssignableFrom(df.getDomainObjectClass()));
 			openDialog.setHelpLocation(new HelpLocation(HelpTopics.PROGRAM, "Open_File_Dialog"));
 			openDialog.addOkActionListener(listener);
 		}

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/datamgr/DataTypesProvider.java

@@ -608,8 +608,15 @@ public class DataTypesProvider extends ComponentProviderAdapter {
 		ArchiveNode archiveNode = dataTypeNode.getArchiveNode();
 
 		if (archiveNode instanceof ProjectArchiveNode && !archiveNode.isModifiable()) {
-			Msg.showInfo(getClass(), archiveGTree, "Archive Not Checked Out",
+			ProjectArchiveNode projectArchive = (ProjectArchiveNode) archiveNode;
-				"You must checkout this archive before you may edit data types.");
+			if (projectArchive.getDomainFile().isReadOnly()) {
+				Msg.showInfo(getClass(), archiveGTree, "Read-Only Archive",
+					"You may not edit data type within a read-only project archive.");
+			}
+			else {
+				Msg.showInfo(getClass(), archiveGTree, "Archive Not Checked Out",
+					"You must checkout this archive before you may edit data types.");
+			}
 			return;
 		}
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/datamgr/actions/associate/AssociateDataTypeAction.java

@@ -38,6 +38,7 @@ import ghidra.app.plugin.core.datamgr.tree.ArchiveNode;
 import ghidra.app.plugin.core.datamgr.tree.DataTypeNode;
 import ghidra.app.plugin.core.datamgr.util.DataTypeTreeCopyMoveTask;
 import ghidra.app.plugin.core.datamgr.util.DataTypeTreeCopyMoveTask.ActionType;
+import ghidra.app.plugin.core.datamgr.util.DataTypeUtils;
 import ghidra.program.model.data.*;
 import ghidra.util.Msg;
 import ghidra.util.layout.PairLayout;
@@ -85,26 +86,21 @@ public class AssociateDataTypeAction extends DockingAction {
 		return !nodes.isEmpty();
 	}
 
-	private boolean hasSingleModifiableSourceArchive(List<GTreeNode> nodes) {
+	private Archive getSingleDTArchive(List<GTreeNode> nodes) {
 
-		Archive sourceArchive = null;
+		Archive dtArchive = null;
 		for (GTreeNode node : nodes) {
 			Archive archive = findArchive(node);
-			if (sourceArchive == null) {
+			if (dtArchive == null) {
-				sourceArchive = archive;
+				dtArchive = archive;
 				continue;
 			}
 
-			if (sourceArchive != archive) {
+			if (dtArchive != archive) {
-				return false;
+				return null;
 			}
 		}
-
+		return dtArchive;
-		if (sourceArchive != null && sourceArchive.isModifiable()) {
-			return true;
-		}
-
-		return false;
 	}
 
 	private static Archive findArchive(GTreeNode node) {
@@ -134,13 +130,20 @@ public class AssociateDataTypeAction extends DockingAction {
 
 		List<GTreeNode> nodes = ((DataTypesActionContext) context).getSelectedNodes();
 
-		if (!hasSingleModifiableSourceArchive(nodes)) {
+		Archive dtArchive = getSingleDTArchive(nodes);
-			Msg.showInfo(this, getProviderComponent(), "Multiple Source Archives",
+		if (dtArchive == null) {
+			Msg.showInfo(this, getProviderComponent(), "Multiple Data Type Archives",
 				"The currently selected nodes are from multiple archives.\n" +
 					"Please select only nodes from a single archvie.");
 			return;
 		}
 
+		if (!dtArchive.isModifiable()) {
+			DataTypeUtils.showUnmodifiableArchiveErrorMessage(context.getSourceComponent(),
+				"Disassociate Failed", dtArchive.getDataTypeManager());
+			return;
+		}
+
 		if (isAlreadyAssociated((DataTypesActionContext) context)) {
 			Msg.showInfo(this, getProviderComponent(), "Already Associated",
 				"One or more of the currently selected nodes are already associated\n" +

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/datamgr/archive/DataTypeManagerHandler.java

@@ -4,9 +4,9 @@
  * 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.
@@ -76,7 +76,7 @@ public class DataTypeManagerHandler {
 	private DataTreeDialog dataTreeSaveDialog;
 	private CreateDataTypeArchiveDataTreeDialog dataTreeCreateDialog;
 	private boolean treeDialogCancelled = false;
-	private DomainFileFilter domainFileFilter;
+	private DomainFileFilter createArchiveFileFilter;
 
 	private DataTypeIndexer dataTypeIndexer;
 	private List<ArchiveManagerListener> archiveManagerlisteners = new ArrayList<>();
@@ -102,9 +102,17 @@ public class DataTypeManagerHandler {
 		dataTypeIndexer.addDataTypeManager(builtInDataTypesManager);
 		openArchives.add(new BuiltInArchive(this, builtInDataTypesManager));
 
-		domainFileFilter = f -> {
+		createArchiveFileFilter = new DomainFileFilter() {
-			Class<?> c = f.getDomainObjectClass();
+
-			return DataTypeArchive.class.isAssignableFrom(c);
+			@Override
+			public boolean accept(DomainFile df) {
+				return DataTypeArchive.class.isAssignableFrom(df.getDomainObjectClass());
+			}
+
+			@Override
+			public boolean followLinkedFolders() {
+				return false;
+			}
 		};
 
 		folderListener = new MyFolderListener();
@@ -1425,7 +1433,7 @@ public class DataTypeManagerHandler {
 				}
 			};
 			dataTreeSaveDialog =
-				new DataTreeDialog(null, "Save As", DataTreeDialog.SAVE, domainFileFilter);
+				new DataTreeDialog(null, "Save As", DataTreeDialog.SAVE, createArchiveFileFilter);
 
 			dataTreeSaveDialog.addOkActionListener(listener);
 			dataTreeSaveDialog
@@ -1465,7 +1473,7 @@ public class DataTypeManagerHandler {
 			};
 
 			dataTreeCreateDialog = new CreateDataTypeArchiveDataTreeDialog(null, "Create",
-				DataTreeDialog.CREATE, domainFileFilter);
+				DataTreeDialog.CREATE, createArchiveFileFilter);
 
 			dataTreeCreateDialog.addOkActionListener(listener);
 			dataTreeCreateDialog.setHelpLocation(

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/datamgr/util/DataTypeUtils.java

@@ -24,6 +24,7 @@ import javax.swing.Icon;
 import generic.theme.GColor;
 import generic.theme.GIcon;
 import ghidra.app.services.DataTypeQueryService;
+import ghidra.program.database.data.ProjectDataTypeManager;
 import ghidra.program.model.data.*;
 import ghidra.program.model.data.Enum;
 import ghidra.util.Msg;
@@ -438,9 +439,18 @@ public class DataTypeUtils {
 			msg = "The archive file is not modifiable!\nYou must open the archive for editing\n" +
 				"before performing this operation.\n" + dtm.getName();
 		}
+		else if (dtm instanceof ProjectDataTypeManager) {
+			ProjectDataTypeManager projectDtm = (ProjectDataTypeManager) dtm;
+			if (!projectDtm.isUpdatable() && !projectDtm.getDomainFile().canCheckout()) {
+				msg = "The project archive is not modifiable!\n" + dtm.getName();
+			}
+			else {
+				msg = "The project archive is not modifiable!\nYou must check out the archive\n" +
+					"before performing this operation.\n" + dtm.getName();
+			}
+		}
 		else {
-			msg = "The project archive is not modifiable!\nYou must check out the archive\n" +
+			msg = "The Archive is not modifiable!\n";
-				"before performing this operation.\n" + dtm.getName();
 		}
 		Msg.showInfo(DataTypeUtils.class, parent, title, msg);
 	}

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/exporter/ExporterDialog.java

@@ -295,11 +295,15 @@ public class ExporterDialog extends DialogComponentProvider implements AddressFa
 		return comboBox;
 	}
 
+	@SuppressWarnings("unchecked")
 	private List<Exporter> getApplicableExporters() {
 		List<Exporter> list = new ArrayList<>(ClassSearcher.getInstances(Exporter.class));
-		Class<? extends DomainObject> domainObjectClass = domainFile.getDomainObjectClass();
+		Class<?> domainObjectClass = domainFile.getDomainObjectClass();
-		list.removeIf(exporter -> !exporter.canExportDomainObject(domainObjectClass));
+		if (DomainObject.class.isAssignableFrom(domainObjectClass)) {
-		Collections.sort(list, (o1, o2) -> o1.toString().compareTo(o2.toString()));
+			list.removeIf(exporter -> !exporter
+					.canExportDomainObject((Class<? extends DomainObject>) domainObjectClass));
+			Collections.sort(list, (o1, o2) -> o1.toString().compareTo(o2.toString()));
+		}
 		return list;
 	}
 
@@ -422,8 +426,16 @@ public class ExporterDialog extends DialogComponentProvider implements AddressFa
 
 	private void doOpenFile(TaskMonitor monitor) {
 		try {
-			domainObject = domainFile.getImmutableDomainObject(this, DomainFile.DEFAULT_VERSION,
+			if (domainFile.isLinkFile()) {
-				TaskMonitor.DUMMY);
+				// Linked files are always subject to upgrade if needed and do not support
+				// getImmutableDomainObject
+				domainObject =
+					domainFile.getReadOnlyDomainObject(this, DomainFile.DEFAULT_VERSION, monitor);
+			}
+			else {
+				domainObject =
+					domainFile.getImmutableDomainObject(this, DomainFile.DEFAULT_VERSION, monitor);
+			}
 		}
 		catch (VersionException | CancelledException | IOException e) {
 			Msg.showError(this, getComponent(), "Error Opening File",

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/misc/MyProgramChangesDisplayPlugin.java

@@ -147,7 +147,8 @@ public class MyProgramChangesDisplayPlugin extends ProgramPlugin implements Doma
 
 			@Override
 			public boolean isEnabledForContext(ActionContext context) {
-				return currentProgram != null && currentProgram.getDomainFile().canCheckin();
+				return currentProgram != null &&
+					currentProgram.getDomainFile().modifiedSinceCheckout();
 			}
 		};
 

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/processors/LanguageProviderPlugin.java

@@ -26,8 +26,8 @@ import docking.action.MenuData;
 import docking.widgets.OptionDialog;
 import ghidra.app.CorePluginPackage;
 import ghidra.app.plugin.PluginCategoryNames;
-import ghidra.framework.main.FrontEndTool;
 import ghidra.framework.main.ApplicationLevelPlugin;
+import ghidra.framework.main.FrontEndTool;
 import ghidra.framework.main.datatable.ProjectDataContext;
 import ghidra.framework.model.*;
 import ghidra.framework.plugintool.*;
@@ -316,18 +316,20 @@ public final class LanguageProviderPlugin extends Plugin implements ApplicationL
 			try {
 				SwingUtilities.invokeAndWait(() -> {
 					ToolServices toolServices = tool.getToolServices();
-					String defaultToolName = toolServices.getDefaultToolTemplate(file).getName();
+					ToolTemplate defaultToolTemplate = toolServices.getDefaultToolTemplate(file);
-					for (PluginTool t : toolServices.getRunningTools()) {
+					if (defaultToolTemplate != null) {
-						if (t.getName().equals(defaultToolName)) {
+						String defaultToolName = defaultToolTemplate.getName();
-							openTool = t;
+						for (PluginTool t : toolServices.getRunningTools()) {
-							break;
+							if (t.getName().equals(defaultToolName)) {
+								openTool = t;
+								break;
+							}
 						}
 					}
-					if (openTool != null) {
+					if (openTool == null ||
-						openTool.acceptDomainFiles(new DomainFile[] { file });
+						!openTool.acceptDomainFiles(new DomainFile[] { file })) {
-					}
+						Msg.showError(this, tool.getToolFrame(), "Failed to Open Program",
-					else {
+							"A suitable default tool could not found!");
-						openTool = tool.getToolServices().launchDefaultTool(file);
 					}
 				});
 			}
@@ -336,7 +338,7 @@ public final class LanguageProviderPlugin extends Plugin implements ApplicationL
 			}
 			catch (InvocationTargetException e) {
 				Throwable t = e.getCause();
-				Msg.showError(this, tool.getToolFrame(), "Tool Launch Failed",
+				Msg.showError(this, tool.getToolFrame(), "Failed to Open Program",
 					"An error occurred while attempting to launch your default tool!", t);
 			}
 		}

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/progmgr/MultiProgramManager.java

@@ -30,6 +30,7 @@ import ghidra.app.events.*;
 import ghidra.app.nav.Navigatable;
 import ghidra.app.services.*;
 import ghidra.app.util.task.OpenProgramTask;
+import ghidra.app.util.task.OpenProgramTask.OpenProgramRequest;
 import ghidra.framework.data.DomainObjectAdapterDB;
 import ghidra.framework.model.*;
 import ghidra.framework.plugintool.PluginTool;
@@ -42,9 +43,6 @@ import ghidra.util.task.TaskLauncher;
 
 class MultiProgramManager implements DomainObjectListener, TransactionListener {
 
-	// arbitrary counter for given ProgramInfo objects and ID to use for sorting
-	private static final AtomicInteger nextAvailableId = new AtomicInteger();
-
 	private ProgramManagerPlugin plugin;
 	private PluginTool tool;
 	private ProgramInfo currentInfo;
@@ -82,25 +80,31 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 		};
 	}
 
-	void addProgram(Program p, URL ghidraURL, int state) {
+	void addProgram(Program p, DomainFile domainFile, int state) {
+		addProgram(new ProgramInfo(p, domainFile, state != ProgramManager.OPEN_HIDDEN), state);
+	}
+
+	void addProgram(Program p, URL ghidraUrl, int state) {
+		addProgram(new ProgramInfo(p, ghidraUrl, state != ProgramManager.OPEN_HIDDEN), state);
+	}
+
+	private void addProgram(ProgramInfo programInfo, int state) {
+		Program p = programInfo.program;
 		ProgramInfo oldInfo = getInfo(p);
 		if (oldInfo == null) {
+			oldInfo = programInfo;
 			p.addConsumer(tool);
-			ProgramInfo info = new ProgramInfo(p, state != ProgramManager.OPEN_HIDDEN);
+			openPrograms.add(oldInfo);
-			info.ghidraURL = ghidraURL;
-			openPrograms.add(info);
 			openPrograms.sort(Comparator.naturalOrder());
-			programMap.put(p, info);
+			programMap.put(p, oldInfo);
 
 			fireOpenEvents(p);
 
 			p.addListener(this);
 			p.addTransactionListener(this);
 		}
-		else {
+		else if (!oldInfo.visible && state != ProgramManager.OPEN_HIDDEN) {
-			if (!oldInfo.visible && state != ProgramManager.OPEN_HIDDEN) {
+			oldInfo.setVisible(true);
-				oldInfo.setVisible(true);
-			}
 		}
 		if (state == ProgramManager.OPEN_CURRENT) {
 			saveLocation();
@@ -246,12 +250,7 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 		TransientToolState toolState = null;
 		if (currentInfo != null) {
 			currentInfo.setVisible(true);
-			DomainFile df = currentInfo.program.getDomainFile();
+			tool.setSubTitle(currentInfo.toString());
-			String title = df.toString();
-			if (df.isReadOnly()) {
-				title = title + " [Read-Only]";
-			}
-			tool.setSubTitle(title);
 			txMonitor.setProgram(currentInfo.program);
 			if (currentInfo.lastState != null) {
 				toolState = currentInfo.lastState;
@@ -370,7 +369,7 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 		return (info != null && info.owner != null);
 	}
 
-	private ProgramInfo getInfo(Program p) {
+	ProgramInfo getInfo(Program p) {
 		if (p == null) {
 			return null;
 		}
@@ -378,9 +377,6 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 	}
 
 	Program getOpenProgram(URL ghidraURL) {
-		if (!GhidraURL.isServerRepositoryURL(ghidraURL)) {
-			return null;
-		}
 		URL normalizedURL = GhidraURL.getNormalizedURL(ghidraURL);
 		for (ProgramInfo info : programMap.values()) {
 			URL url = info.ghidraURL;
@@ -392,10 +388,10 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 	}
 
 	Program getOpenProgram(DomainFile domainFile, int version) {
-		for (Program program : programMap.keySet()) {
+		for (ProgramInfo info : programMap.values()) {
-			DomainFile programDomainFile = program.getDomainFile();
+			DomainFile df = info.domainFile;
-			if (filesMatch(domainFile, version, programDomainFile)) {
+			if (df != null && filesMatch(domainFile, version, df)) {
-				return program;
+				return info.program;
 			}
 		}
 		return null;
@@ -413,7 +409,7 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 		if (!SystemUtilities.isEqual(file1.getProjectLocator(), file2.getProjectLocator())) {
 			return false;
 		}
-
+		// TODO: version check is questionable - unclear how proxy file would work
 		int openVersion = file2.isReadOnly() ? file2.getVersion() : -1;
 		return version == openVersion;
 	}
@@ -488,28 +484,54 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 			OpenProgramTask openTask = new OpenProgramTask(file, -1, this);
 			openTask.setSilent();
 			new TaskLauncher(openTask, tool.getToolFrame());
-			Program openProgram = openTask.getOpenProgram();
+			OpenProgramRequest openProgramReq = openTask.getOpenProgram();
-			plugin.openProgram(openProgram,
+			if (openProgramReq != null) {
-				dataState != null ? ProgramManager.OPEN_CURRENT : ProgramManager.OPEN_VISIBLE);
+				plugin.openProgram(openProgramReq.getProgram(),
-			openProgram.release(this);
+					dataState != null ? ProgramManager.OPEN_CURRENT : ProgramManager.OPEN_VISIBLE);
-			removeProgram((Program) oldObject);
+				openProgramReq.release();
-			if (dataState != null) {
+				removeProgram((Program) oldObject);
-				tool.restoreDataStateFromXml(dataState);
+				if (dataState != null) {
+					tool.restoreDataStateFromXml(dataState);
+				}
 			}
 		}
 	}
 
-	private class ProgramInfo implements Comparable<ProgramInfo> {
+	class ProgramInfo implements Comparable<ProgramInfo> {
+
+		// arbitrary counter for given ProgramInfo objects and ID to use for sorting
+		private static final AtomicInteger nextAvailableId = new AtomicInteger();
+
+		public final Program program;
+		
+		// NOTE: domainFile and ghidraURL use are mutually exclusive and reflect how program was
+		// opened.  Supported cases include:
+		// 1. Opened via Program file
+		// 2. Opened via ProgramLink file
+		// 3. Opened via Program URL
+		
+		public final DomainFile domainFile; // may be link file
+		public final URL ghidraURL;
 
-		private Program program;
-		private URL ghidraURL;
 		private TransientToolState lastState;
 		private int instance;
-		private boolean visible;
+		private boolean visible = false;
 		private Object owner;
 
-		ProgramInfo(Program p, boolean visible) {
+		private String str; // cached toString
+
+		ProgramInfo(Program p, DomainFile domainFile, boolean visible) {
 			this.program = p;
+			this.domainFile = domainFile;
+			this.ghidraURL = null;
+			this.visible = visible;
+			instance = nextAvailableId.incrementAndGet();
+		}
+		
+		ProgramInfo(Program p, URL ghidraURL, boolean visible) {
+			this.program = p;
+			this.domainFile = null;
+			this.ghidraURL = ghidraURL;
 			this.visible = visible;
 			instance = nextAvailableId.incrementAndGet();
 		}
@@ -523,5 +545,24 @@ class MultiProgramManager implements DomainObjectListener, TransactionListener {
 		public int compareTo(ProgramInfo info) {
 			return instance - info.instance;
 		}
+
+		@Override
+		public String toString() {
+			if (str != null) {
+				return str;
+			}
+			StringBuilder buf = new StringBuilder();
+			DomainFile df = program.getDomainFile();
+			if (domainFile != null && domainFile.isLinkFile()) {
+				buf.append(domainFile.getName());
+				buf.append("->");
+			}
+			buf.append(df.toString());
+			if (df.isReadOnly()) {
+				buf.append(" [Read-Only]");
+			}
+			str = buf.toString();
+			return str;
+		}
 	}
 }

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/progmgr/ProgramManagerPlugin.java

@@ -18,7 +18,6 @@ package ghidra.app.plugin.core.progmgr;
 import java.awt.Component;
 import java.awt.event.ActionListener;
 import java.beans.PropertyEditor;
-import java.io.IOException;
 import java.net.MalformedURLException;
 import java.net.URL;
 import java.util.ArrayList;
@@ -32,26 +31,26 @@ import ghidra.app.CorePluginPackage;
 import ghidra.app.context.ProgramActionContext;
 import ghidra.app.events.*;
 import ghidra.app.plugin.PluginCategoryNames;
+import ghidra.app.plugin.core.progmgr.MultiProgramManager.ProgramInfo;
 import ghidra.app.services.ProgramManager;
 import ghidra.app.util.HelpTopics;
 import ghidra.app.util.NamespaceUtils;
 import ghidra.app.util.task.OpenProgramTask;
+import ghidra.app.util.task.OpenProgramTask.OpenProgramRequest;
 import ghidra.framework.client.ClientUtil;
-import ghidra.framework.data.ProjectFileManager;
 import ghidra.framework.main.OpenVersionedFileDialog;
 import ghidra.framework.model.*;
 import ghidra.framework.options.*;
 import ghidra.framework.plugintool.*;
 import ghidra.framework.plugintool.util.PluginStatus;
-import ghidra.framework.protocol.ghidra.*;
+import ghidra.framework.protocol.ghidra.GhidraURL;
-import ghidra.program.database.ProgramContentHandler;
 import ghidra.program.model.address.*;
 import ghidra.program.model.listing.Program;
 import ghidra.program.model.symbol.Symbol;
 import ghidra.program.model.symbol.SymbolType;
 import ghidra.program.util.*;
 import ghidra.util.*;
-import ghidra.util.exception.NotFoundException;
+import ghidra.util.exception.AssertException;
 import ghidra.util.task.TaskLauncher;
 
 //@formatter:off
@@ -121,16 +120,21 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 			if (domainFile == null) {
 				continue;
 			}
-			if (!(Program.class.isAssignableFrom(domainFile.getDomainObjectClass()))) {
+			Class<? extends DomainObject> domainObjectClass = domainFile.getDomainObjectClass();
-				continue;
+			if (Program.class.isAssignableFrom(domainObjectClass)) {
+				filesToOpen.add(domainFile);
 			}
-			filesToOpen.add(domainFile);
 		}
 		openPrograms(filesToOpen);
 
 		return !filesToOpen.isEmpty();
 	}
 
+	@Override
+	public boolean accept(URL url) {
+		return openProgram(url, OPEN_CURRENT) != null;
+	}
+
 	@Override
 	public Class<?>[] getSupportedDataTypes() {
 		return new Class[] { Program.class };
@@ -144,89 +148,53 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 			return null;
 		}
 
-		return Swing.runNow(() -> doOpenProgram(ghidraURL, state));
+		// Check for URL already open and re-use
-	}
+		URL url = GhidraURL.getNormalizedURL(ghidraURL);
-
+		Program p = programMgr.getOpenProgram(url);
-	private void messageBadProgramURL(URL ghidraURL) {
+		if (p != null) {
-		Msg.showError(this, null, "Invalid Ghidra URL",
+			showProgram(p, url, state);
-			"Ghidra URL does not reference a Ghidra Program: " + ghidraURL);
+			if (state == ProgramManager.OPEN_CURRENT) {
-	}
+				gotoProgramRef(p, ghidraURL.getRef());
-
-	protected Program doOpenProgram(URL ghidraURL, int openState) {
-		if (!GhidraURL.isServerRepositoryURL(ghidraURL)) {
-			Msg.showError(this, null, "Invalid Ghidra URL",
-				"Ghidra URL does not reference a Ghidra Program: " + ghidraURL);
-			return null;
-		}
-		Program openProgram = programMgr.getOpenProgram(ghidraURL);
-		if (openProgram != null) {
-			programMgr.addProgram(openProgram, GhidraURL.getNormalizedURL(ghidraURL), openState);
-			if (openState == ProgramManager.OPEN_CURRENT) {
-				gotoProgramRef(openProgram, ghidraURL.getRef());
 				programMgr.saveLocation();
 			}
-			contextChanged();
+			return p;
-			return openProgram;
 		}
 
-		GhidraURLWrappedContent wrappedContent = null;
+		Program program = Swing.runNow(() -> doOpenProgram(ghidraURL, state));
-		Object content = null;
+
+		if (program != null) {
+			Msg.info(this, "Opened program in " + tool.getName() + " tool: " + ghidraURL);
+		}
+		return program;
+	}
+
+	/**
+	 * Open GhidraURL which corresponds to {@code ghidra://} remote URLs which correspond to a 
+	 * repository program file.
+	 * @param ghidraURL Ghidra URL which specified Program to be opened which optional ref
+	 * @param openState open state 
+	 * @return program instance of null if open failed
+	 */
+	private Program doOpenProgram(URL ghidraURL, int openState) {
+		Program p = null;
 		try {
-			GhidraURLConnection c = (GhidraURLConnection) ghidraURL.openConnection();
+			URL url = GhidraURL.getNormalizedURL(ghidraURL);
-			Object obj = c.getContent();
+			OpenProgramTask task = new OpenProgramTask(url, this);
-			if (c.getResponseCode() == GhidraURLConnection.GHIDRA_UNAUTHORIZED) {
+			new TaskLauncher(task, tool.getToolFrame());
-				return null; // assume user already notified
+			OpenProgramRequest openProgramReq = task.getOpenProgram();
+			if (openProgramReq != null) {
+				p = openProgramReq.getProgram();
+				showProgram(p, url, openState);
+				openProgramReq.release();
 			}
-			if (!(obj instanceof GhidraURLWrappedContent)) {
-				messageBadProgramURL(ghidraURL);
-				return null;
-			}
-			wrappedContent = (GhidraURLWrappedContent) obj;
-			content = wrappedContent.getContent(this);
-			if (!(content instanceof DomainFile)) {
-				messageBadProgramURL(ghidraURL);
-				return null;
-			}
-			DomainFile df = (DomainFile) content;
-			if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(df.getContentType())) {
-				messageBadProgramURL(ghidraURL);
-				return null;
-			}
-
-			OpenProgramTask task = new OpenProgramTask(df, true, this);
-			TaskLauncher.launch(task);
-
-			openProgram = task.getOpenProgram();
-			if (openProgram == null) {
-				return null;
-			}
-
-			programMgr.addProgram(openProgram, GhidraURL.getNormalizedURL(ghidraURL), openState);
-			contextChanged();
-			openProgram.release(this);
-			if (openState == ProgramManager.OPEN_CURRENT) {
-				gotoProgramRef(openProgram, ghidraURL.getRef());
-				programMgr.saveLocation();
-			}
-			return openProgram;
-		}
-		catch (NotFoundException e) {
-			messageBadProgramURL(ghidraURL);
-		}
-		catch (MalformedURLException e) {
-			Msg.showError(this, null, "Invalid Ghidra URL",
-				"Improperly formed Ghidra URL: " + ghidraURL);
-		}
-		catch (IOException e) {
-			Msg.showError(this, null, "Program Open Failed",
-				"Failed to open Ghidra URL: " + e.getMessage());
 		}
 		finally {
-			if (content != null) {
+			if (p != null && openState == ProgramManager.OPEN_CURRENT) {
-				wrappedContent.release(content, this);
+				gotoProgramRef(p, ghidraURL.getRef());
+				programMgr.saveLocation();
 			}
 		}
-		return null;
+		return p;
 	}
 
 	private boolean gotoProgramRef(Program program, String ref) {
@@ -296,9 +264,7 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 		}
 
 		Program program = Swing.runNow(() -> {
-			Program p = doOpenProgram(domainFile, version, state);
+			return doOpenProgram(domainFile, version, state);
-			contextChanged();
-			return p;
 		});
 
 		if (program != null) {
@@ -460,13 +426,39 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 
 	@Override
 	public void openProgram(final Program program, final int state) {
+		showProgram(program, program.getDomainFile(), state);
+	}
+
+	private void showProgram(Program p, URL ghidraUrl, final int state) {
+		if (p == null || p.isClosed()) {
+			throw new AssertException("Opened program required");
+		}
 		if (locked) {
 			throw new IllegalStateException(
 				"Progam manager is locked and cannot accept a new program");
 		}
 
 		Runnable r = () -> {
-			programMgr.addProgram(program, null, state);
+			programMgr.addProgram(p, ghidraUrl, state);
+			if (state == ProgramManager.OPEN_CURRENT) {
+				programMgr.saveLocation();
+			}
+			contextChanged();
+		};
+		Swing.runNow(r);
+	}
+
+	private void showProgram(Program p, DomainFile domainFile, final int state) {
+		if (p == null || p.isClosed()) {
+			throw new AssertException("Opened program required");
+		}
+		if (locked) {
+			throw new IllegalStateException(
+				"Progam manager is locked and cannot accept a new program");
+		}
+
+		Runnable r = () -> {
+			programMgr.addProgram(p, domainFile, state);
 			if (state == ProgramManager.OPEN_CURRENT) {
 				programMgr.saveLocation();
 			}
@@ -625,11 +617,9 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 					doOpenProgram(domainFile, version, OPEN_CURRENT);
 				}
 			};
-			DomainFileFilter filter = f -> {
+			openDialog = new OpenVersionedFileDialog(tool, "Open Program", f -> {
-				Class<?> c = f.getDomainObjectClass();
+				return Program.class.isAssignableFrom(f.getDomainObjectClass());
-				return Program.class.isAssignableFrom(c);
+			});
-			};
-			openDialog = new OpenVersionedFileDialog(tool, "Open Program", filter);
 			openDialog.setHelpLocation(new HelpLocation(HelpTopics.PROGRAM, "Open_File_Dialog"));
 			openDialog.addOkActionListener(listener);
 		}
@@ -638,9 +628,12 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 	}
 
 	public void openPrograms(List<DomainFile> filesToOpen) {
+		Program showIfNeeded = null;
 		OpenProgramTask openTask = null;
 		for (DomainFile domainFile : filesToOpen) {
-			if (programMgr.getOpenProgram(domainFile, -1) != null) {
+			Program p = programMgr.getOpenProgram(domainFile, -1);
+			if (p != null) {
+				showIfNeeded = p;
 				continue;
 			}
 			if (openTask == null) {
@@ -652,32 +645,37 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 		}
 		if (openTask != null) {
 			new TaskLauncher(openTask, tool.getToolFrame());
-			List<Program> openPrograms = openTask.getOpenPrograms();
+			List<OpenProgramRequest> openProgramReqs = openTask.getOpenPrograms();
-
+			boolean isFirst = true;
-			for (Program program : openPrograms) {
+			for (OpenProgramRequest programReq : openProgramReqs) {
-				openProgram(program, OPEN_VISIBLE);
+				showProgram(programReq.getProgram(), programReq.getDomainFile(),
-				program.release(this);
+					isFirst ? OPEN_CURRENT : OPEN_VISIBLE);
-			}
+				programReq.release();
-			if (!openPrograms.isEmpty()) {
+				isFirst = false;
-				openProgram(openPrograms.get(0), OPEN_CURRENT);
+				showIfNeeded = null;
 			}
 		}
+		if (showIfNeeded != null) {
+			showProgram(showIfNeeded, showIfNeeded.getDomainFile(), OPEN_CURRENT);
+		}
 	}
 
 	protected Program doOpenProgram(DomainFile domainFile, int version, int openState) {
-		Program openProgram = programMgr.getOpenProgram(domainFile, version);
+		Program p = programMgr.getOpenProgram(domainFile, version);
-		if (openProgram != null) {
+		if (p != null) {
-			openProgram(openProgram, openState);
+			openProgram(p, openState);
-			return openProgram;
 		}
-		OpenProgramTask task = new OpenProgramTask(domainFile, version, this);
+		else {
-		new TaskLauncher(task, tool.getToolFrame());
+			OpenProgramTask task = new OpenProgramTask(domainFile, version, this);
-		openProgram = task.getOpenProgram();
+			new TaskLauncher(task, tool.getToolFrame());
-		if (openProgram != null) {
+			OpenProgramRequest programReq = task.getOpenProgram();
-			openProgram(openProgram, openState);
+			if (programReq != null) {
-			openProgram.release(this);
+				p = programReq.getProgram();
+				showProgram(p, programReq.getDomainFile(), openState);
+				programReq.release();
+			}
 		}
-		return openProgram;
+		return p;
 	}
 
 	@Override
@@ -705,18 +703,20 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 	 */
 	@Override
 	public void writeDataState(SaveState saveState) {
-		// Only remember programs from non-transient projects
+
-		ArrayList<Program> programs = new ArrayList<>();
+		ArrayList<ProgramInfo> programInfos = new ArrayList<>();
 		for (Program p : programMgr.getAllPrograms()) {
-			ProjectLocator projectLocator = p.getDomainFile().getProjectLocator();
+			ProgramInfo info = programMgr.getInfo(p);
-			if (projectLocator != null && !projectLocator.isTransient()) {
+			if (info != null) {
-				programs.add(p);
+				programInfos.add(info);
 			}
 		}
-		saveState.putInt("NUM_PROGRAMS", programs.size());
+
+		saveState.putInt("NUM_PROGRAMS", programInfos.size());
+
 		int i = 0;
-		for (Program p : programs) {
+		for (ProgramInfo programInfo : programInfos) {
-			writeProgramInfo(p, saveState, i++);
+			writeProgramInfo(programInfo, saveState, i++);
 		}
 		Program p = programMgr.getCurrentProgram();
 		if (p != null) {
@@ -768,13 +768,21 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 		}
 	}
 
-	private void writeProgramInfo(Program program, SaveState saveState, int index) {
+	private void writeProgramInfo(ProgramInfo programInfo, SaveState saveState, int index) {
 		if (locked) {
 			return; // do not save state when locked.
 		}
+
+		if (programInfo.ghidraURL != null) {
+			saveState.putString("URL_" + index, programInfo.ghidraURL.toString());
+			return;
+		}
+
 		String projectLocation = null;
 		String projectName = null;
 		String path = null;
+
+		Program program = programInfo.program;
 		DomainFile df = program.getDomainFile();
 		ProjectLocator projectLocator = df.getProjectLocator();
 		if (projectLocator != null && !projectLocator.isTransient()) {
@@ -797,28 +805,30 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 	 * Read in my data state.
 	 */
 	private void loadPrograms(SaveState saveState) {
+
 		int n = saveState.getInt("NUM_PROGRAMS", 0);
 		if (n == 0) {
 			return;
 		}
-		OpenProgramTask openTask = null;
+		OpenProgramTask openTask = new OpenProgramTask(this);
 
 		for (int index = 0; index < n; index++) {
+
+			URL url = getGhidraURL(saveState, index);
+			if (url != null) {
+				openTask.addProgramToOpen(url);
+				continue;
+			}
+
 			DomainFile domainFile = getDomainFile(saveState, index);
 			if (domainFile == null) {
 				continue;
 			}
 			int version = getVersion(saveState, index);
-
+			openTask.addProgramToOpen(domainFile, version);
-			if (openTask == null) {
-				openTask = new OpenProgramTask(domainFile, version, this);
-			}
-			else {
-				openTask.addProgramToOpen(domainFile, version);
-			}
 		}
 
-		if (openTask == null) {
+		if (!openTask.hasOpenProgramRequests()) {
 			return;
 		}
 
@@ -835,10 +845,29 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 				"Can't open program", e);
 		}
 
-		List<Program> openPrograms = openTask.getOpenPrograms();
+		List<OpenProgramRequest> openProgramReqs = openTask.getOpenPrograms();
-		for (Program program : openPrograms) {
+		for (OpenProgramRequest programReq : openProgramReqs) {
-			openProgram(program, OPEN_VISIBLE);
+			DomainFile df = programReq.getDomainFile();
-			program.release(this);
+			if (df != null) {
+				showProgram(programReq.getProgram(), df, OPEN_VISIBLE);
+			}
+			else {
+				showProgram(programReq.getProgram(), programReq.getGhidraURL(), OPEN_VISIBLE);
+			}
+			programReq.release();
+		}
+	}
+
+	private URL getGhidraURL(SaveState saveState, int index) {
+		String url = saveState.getString("URL_" + index, null);
+		if (url == null) {
+			return null;
+		}
+		try {
+			return new URL(url);
+		}
+		catch (MalformedURLException e) {
+			return null;
 		}
 	}
 
@@ -853,20 +882,7 @@ public class ProgramManagerPlugin extends Plugin implements ProgramManager {
 
 		ProjectData projectData = tool.getProject().getProjectData(projectLocator);
 		if (projectData == null) {
-			// Viewed project not available
+			return null;
-			try {
-				projectData = new ProjectFileManager(projectLocator, false, false);
-			}
-			catch (NotOwnerException e) {
-				Msg.showError(this, tool.getToolFrame(), "Program Open Failed",
-					"Not project owner: " + projectLocator + "(" + pathname + ")");
-				return null;
-			}
-			catch (IOException e) {
-				Msg.showError(this, tool.getToolFrame(), "Program Open Failed",
-					"Project error: " + e.getMessage());
-				return null;
-			}
 		}
 
 		DomainFile df = projectData.getFile(pathname);

Ghidra/Features/Base/src/main/java/ghidra/app/plugin/core/progmgr/ProgramSaveManager.java

@@ -45,9 +45,17 @@ class ProgramSaveManager {
 	ProgramSaveManager(PluginTool tool, ProgramManager programMgr) {
 		this.tool = tool;
 		this.programMgr = programMgr;
-		domainFileFilter = f -> {
+		domainFileFilter = new DomainFileFilter() {
-			Class<?> c = f.getDomainObjectClass();
+
-			return Program.class.isAssignableFrom(c);
+			@Override
+			public boolean accept(DomainFile df) {
+				return Program.class.isAssignableFrom(df.getDomainObjectClass());
+			}
+
+			@Override
+			public boolean followLinkedFolders() {
+				return false; // can't save to linked-folder (read-only)
+			}
 		};
 	}
 
@@ -244,7 +252,8 @@ class ProgramSaveManager {
 			return;
 		}
 		if (existingFile != null) {
-			String msg = "Program " + name + " already exists.\n" + "Do you want to overwrite it?";
+			String msg = existingFile.getContentType() + " file " + name + " already exists.\n" +
+				"Do you want to overwrite it?";
 			if (OptionDialog.showOptionDialog(tool.getToolFrame(), "Duplicate Name", msg,
 				"Overwrite", OptionDialog.QUESTION_MESSAGE) == OptionDialog.CANCEL_OPTION) {
 				return;

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

@@ -312,7 +312,7 @@ public class HeadlessAnalyzer {
 			Object obj = c.getContent();
 			if (!(obj instanceof GhidraURLWrappedContent)) {
 				throw new IOException(
-					"Connect to repository folder failed. Response code: " + c.getResponseCode());
+					"Connect to repository folder failed. Response code: " + c.getStatusCode());
 			}
 			GhidraURLWrappedContent wrappedContent = (GhidraURLWrappedContent) obj;
 			Object content = null;
@@ -336,7 +336,7 @@ public class HeadlessAnalyzer {
 					processWithImport(folder.getPathname(), filesToImport);
 				}
 			}
-			catch (NotFoundException e) {
+			catch (FileNotFoundException e) {
 				throw new IOException("Connect to repository folder failed");
 			}
 			finally {
@@ -369,7 +369,8 @@ public class HeadlessAnalyzer {
 	 * @param rootFolderPath root folder for imports
 	 * @param filesToImport directories and files to be imported (null or empty is acceptable if
 	 *        				we are in -process mode)
-	 * @throws IOException if there was an IO-related problem
+	 * @throws IOException if there was an IO-related problem.  If caused by a failure to obtain a 
+	 * write-lock on the project the exception cause will a {@code LockException}.
 	 */
 	public void processLocal(String projectLocation, String projectName, String rootFolderPath,
 			List<File> filesToImport) throws IOException {
@@ -1107,6 +1108,8 @@ public class HeadlessAnalyzer {
 			return;
 		}
 
+		// Do not follow folder-links or consider program links.  Using content type
+		// to filter is best way to control this.
 		if (!ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
 			return; // skip non-Program files
 		}
@@ -1275,6 +1278,8 @@ public class HeadlessAnalyzer {
 
 		for (DomainFile domFile : parentFolder.getFiles()) {
 			if (filenamePattern == null || filenamePattern.matcher(domFile.getName()).matches()) {
+				// Do not follow folder-links or consider program links.  Using content type
+				// to filter is best way to control this.
 				if (ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
 					filesProcessed = true;
 					processFileNoImport(domFile);
@@ -1308,6 +1313,8 @@ public class HeadlessAnalyzer {
 		boolean filesProcessed = false;
 
 		DomainFile domFile = parentFolder.getFile(filename);
+		// Do not follow folder-links or consider program links.  Using content type
+		// to filter is best way to control this.
 		if (domFile != null &&
 			ProgramContentHandler.PROGRAM_CONTENT_TYPE.equals(domFile.getContentType())) {
 			filesProcessed = true;

Ghidra/Features/Base/src/main/java/ghidra/app/util/task/OpenProgramTask.java

@@ -16,8 +16,9 @@
 package ghidra.app.util.task;
 
 import java.io.IOException;
-import java.util.ArrayList;
+import java.net.MalformedURLException;
-import java.util.List;
+import java.net.URL;
+import java.util.*;
 
 import docking.widgets.OptionDialog;
 import ghidra.app.util.dialog.CheckoutDialog;
@@ -25,8 +26,11 @@ import ghidra.framework.client.ClientUtil;
 import ghidra.framework.client.RepositoryAdapter;
 import ghidra.framework.main.AppInfo;
 import ghidra.framework.model.DomainFile;
+import ghidra.framework.protocol.ghidra.*;
+import ghidra.framework.protocol.ghidra.GhidraURLConnection.StatusCode;
 import ghidra.framework.remote.User;
 import ghidra.framework.store.ExclusiveCheckoutException;
+import ghidra.program.database.ProgramLinkContentHandler;
 import ghidra.program.model.lang.LanguageNotFoundException;
 import ghidra.program.model.listing.Program;
 import ghidra.util.*;
@@ -37,8 +41,8 @@ import ghidra.util.task.TaskMonitor;
 
 public class OpenProgramTask extends Task {
 
-	private final List<DomainFileInfo> domainFileInfoList = new ArrayList<>();
+	private final List<OpenProgramRequest> openProgramRequests = new ArrayList<>();
-	private List<Program> programList = new ArrayList<>();
+	private List<OpenProgramRequest> openedProgramList = new ArrayList<>();
 
 	private final Object consumer;
 	private boolean silent; // if true operation does not permit interaction
@@ -46,11 +50,16 @@ public class OpenProgramTask extends Task {
 
 	private String openPromptText = "Open";
 
+	public OpenProgramTask(Object consumer) {
+		super("Open Program(s)", true, false, true);
+		this.consumer = consumer;
+	}
+
 	public OpenProgramTask(DomainFile domainFile, int version, boolean forceReadOnly,
 			Object consumer) {
 		super("Open Program(s)", true, false, true);
 		this.consumer = consumer;
-		domainFileInfoList.add(new DomainFileInfo(domainFile, version, forceReadOnly));
+		openProgramRequests.add(new OpenProgramRequest(domainFile, version, forceReadOnly));
 	}
 
 	public OpenProgramTask(DomainFile domainFile, int version, Object consumer) {
@@ -65,17 +74,10 @@ public class OpenProgramTask extends Task {
 		this(domainFile, DomainFile.DEFAULT_VERSION, false, consumer);
 	}
 
-	public OpenProgramTask(List<DomainFile> domainFileList, boolean forceReadOnly,
+	public OpenProgramTask(URL ghidraURL, Object consumer) {
-			Object consumer) {
+		super("Open Program(s)", true, false, true);
-		super("Open Program(s)", true, domainFileList.size() > 1, true);
 		this.consumer = consumer;
-		for (DomainFile domainFile : domainFileList) {
+		openProgramRequests.add(new OpenProgramRequest(ghidraURL));
-			domainFileInfoList.add(new DomainFileInfo(domainFile, -1, forceReadOnly));
-		}
-	}
-
-	public OpenProgramTask(List<DomainFile> domainFileList, Object consumer) {
-		this(domainFileList, false, consumer);
 	}
 
 	public void setOpenPromptText(String text) {
@@ -88,7 +90,16 @@ public class OpenProgramTask extends Task {
 
 	public void addProgramToOpen(DomainFile domainFile, int version, boolean forceReadOnly) {
 		setHasProgress(true);
-		domainFileInfoList.add(new DomainFileInfo(domainFile, version, forceReadOnly));
+		openProgramRequests.add(new OpenProgramRequest(domainFile, version, forceReadOnly));
+	}
+
+	public void addProgramToOpen(URL ghidraURL) {
+		setHasProgress(true);
+		openProgramRequests.add(new OpenProgramRequest(ghidraURL));
+	}
+
+	public boolean hasOpenProgramRequests() {
+		return !openProgramRequests.isEmpty();
 	}
 
 	/**
@@ -110,100 +121,97 @@ public class OpenProgramTask extends Task {
 		this.noCheckout = true;
 	}
 
-	public List<Program> getOpenPrograms() {
+	/**
-		return programList;
+	 * Get all successful open program requests
+	 * @return all successful open program requests
+	 */
+	public List<OpenProgramRequest> getOpenPrograms() {
+		return Collections.unmodifiableList(openedProgramList);
 	}
 
-	public Program getOpenProgram() {
+	/**
-		if (programList.isEmpty()) {
+	 * Get the first successful open program request
+	 * @return first successful open program request or null if none
+	 */
+	public OpenProgramRequest getOpenProgram() {
+		if (openedProgramList.isEmpty()) {
 			return null;
 		}
-		return programList.get(0);
+		return openedProgramList.get(0);
 	}
 
 	@Override
 	public void run(TaskMonitor monitor) {
 
-		taskMonitor.initialize(domainFileInfoList.size());
+		taskMonitor.initialize(openProgramRequests.size());
 
-		for (DomainFileInfo domainFileInfo : domainFileInfoList) {
+		for (OpenProgramRequest domainFileInfo : openProgramRequests) {
 			if (taskMonitor.isCancelled()) {
 				return;
 			}
-			openDomainFile(domainFileInfo);
+			domainFileInfo.open();
-
 			taskMonitor.incrementProgress(1);
 		}
 	}
 
-	private void openDomainFile(DomainFileInfo domainFileInfo) {
+	private Object openReadOnlyFile(DomainFile domainFile, URL url, int version) {
-		int version = domainFileInfo.getVersion();
-		DomainFile domainFile = domainFileInfo.getDomainFile();
-		if (version != DomainFile.DEFAULT_VERSION) {
-			openVersionedFile(domainFile, version);
-		}
-		else if (domainFileInfo.isReadOnly()) {
-			openReadOnlyFile(domainFile, version);
-		}
-		else {
-			openUnversionedFile(domainFile);
-		}
-	}
-
-	private void openReadOnlyFile(DomainFile domainFile, int version) {
 		taskMonitor.setMessage("Opening " + domainFile.getName());
-		openReadOnly(domainFile, version);
+		return openReadOnly(domainFile, url, version);
 	}
 
-	private void openVersionedFile(DomainFile domainFile, int version) {
+	private Object openVersionedFile(DomainFile domainFile, URL url, int version) {
 		taskMonitor.setMessage("Getting Version " + version + " for " + domainFile.getName());
-		openReadOnly(domainFile, version);
+		return openReadOnly(domainFile, url, version);
 	}
 
-	private void openReadOnly(DomainFile domainFile, int version) {
+	private Object openReadOnly(DomainFile domainFile, URL url, int version) {
-		String contentType = null;
+		String contentType = domainFile.getContentType();
+		String path = url != null ? url.toString() : domainFile.getPathname();
+		Object obj = null;
 		try {
-			contentType = domainFile.getContentType();
-			Program program =
-				(Program) domainFile.getReadOnlyDomainObject(consumer, version, taskMonitor);
 
-			if (program == null) {
+			obj = domainFile.getReadOnlyDomainObject(consumer, version, taskMonitor);
-				String errorMessage = "Can't open program - \"" + domainFile.getPathname() + "\"";
+
+			if (obj == null) {
+				String errorMessage = "Can't open " + contentType + " - \"" + path + "\"";
 				if (version != DomainFile.DEFAULT_VERSION) {
 					errorMessage += " version " + version;
 				}
 
-				Msg.showError(this, null, "DomainFile Not Found", errorMessage);
+				Msg.showError(this, null, "File Not Found", errorMessage);
-			}
-			else {
-				programList.add(program);
 			}
+			
 		}
 		catch (CancelledException e) {
 			// we don't care, the task has been cancelled
 		}
 		catch (IOException e) {
-			if (domainFile.isInWritableProject()) {
+			if (url == null && domainFile.isInWritableProject()) {
 				ClientUtil.handleException(AppInfo.getActiveProject().getRepository(), e,
-					"Get Versioned Object", null);
+					"Get " + contentType, null);
+			}
+			else if (version != DomainFile.DEFAULT_VERSION) {
+				Msg.showError(this, null, "Error Getting Versioned Program",
+					"Could not get version " + version + " for " + path, e);
 			}
 			else {
-				Msg.showError(this, null, "Error Getting Versioned Object",
+				Msg.showError(this, null, "Error Getting Program",
-					"Could not get version " + version + " for " + domainFile.getName(), e);
+					"Open program failed for " + path, e);
 			}
 		}
 		catch (VersionException e) {
 			VersionExceptionHandler.showVersionError(null, domainFile.getName(), contentType,
 				"Open", e);
 		}
+		return obj;
 	}
 
-	private void openUnversionedFile(DomainFile domainFile) {
+	private Program openUnversionedFile(DomainFile domainFile) {
 		String filename = domainFile.getName();
 		taskMonitor.setMessage("Opening " + filename);
 		performOptionalCheckout(domainFile);
 		try {
-			openFileMaybeUgrade(domainFile);
+			return openFileMaybeUgrade(domainFile);
 		}
 		catch (VersionException e) {
 			String contentType = domainFile.getContentType();
@@ -226,9 +234,10 @@ public class OpenProgramTask extends Task {
 					"Getting domain object failed.\n" + e.getMessage(), e);
 			}
 		}
+		return null;
 	}
 
-	private void openFileMaybeUgrade(DomainFile domainFile)
+	private Program openFileMaybeUgrade(DomainFile domainFile)
 			throws IOException, CancelledException, VersionException {
 
 		boolean recoverFile = false;
@@ -236,24 +245,18 @@ public class OpenProgramTask extends Task {
 			recoverFile = askRecoverFile(domainFile.getName());
 		}
 
+		Program program = null;
 		try {
-			Program program =
+			program =
 				(Program) domainFile.getDomainObject(consumer, false, recoverFile, taskMonitor);
-
-			if (program != null) {
-				programList.add(program);
-			}
-
 		}
 		catch (VersionException e) {
 			if (VersionExceptionHandler.isUpgradeOK(null, domainFile, openPromptText, e)) {
-				Program program =
+				program =
 					(Program) domainFile.getDomainObject(consumer, true, recoverFile, taskMonitor);
-				if (program != null) {
-					programList.add(program);
-				}
 			}
 		}
+		return program;
 	}
 
 	private boolean askRecoverFile(final String filename) {
@@ -294,32 +297,158 @@ public class OpenProgramTask extends Task {
 		}
 	}
 
-	static class DomainFileInfo {
+	public class OpenProgramRequest {
-		private final DomainFile domainFile;
-		private final int version;
-		private boolean forceReadOnly;
 
-		public DomainFileInfo(DomainFile domainFile, int version, boolean forceReadOnly) {
+		// ghidraURL and domainFile use are mutually exclusive
+		private final URL ghidraURL;
+		private final DomainFile domainFile;
+
+		private URL linkURL; // link URL read from domainFile
+
+		private final int version;
+		private final boolean forceReadOnly;
+		private Program program;
+
+		public OpenProgramRequest(URL ghidraURL) {
+			if (!GhidraURL.PROTOCOL.equals(ghidraURL.getProtocol())) {
+				throw new IllegalArgumentException(
+					"unsupported protocol: " + ghidraURL.getProtocol());
+			}
+			this.ghidraURL = ghidraURL;
+			this.domainFile = null;
+			this.version = -1;
+			this.forceReadOnly = true;
+		}
+
+		public OpenProgramRequest(DomainFile domainFile, int version, boolean forceReadOnly) {
 			this.domainFile = domainFile;
+			this.ghidraURL = null;
 			this.version =
 				(domainFile.isReadOnly() && domainFile.isVersioned()) ? domainFile.getVersion()
 						: version;
 			this.forceReadOnly = forceReadOnly;
 		}
 
-		public boolean isReadOnly() {
+		/**
-			return forceReadOnly || domainFile.isReadOnly() ||
+		 * Get the {@link DomainFile} which corresponds to program open request.  This will be
-				version != DomainFile.DEFAULT_VERSION;
+		 * null for all URL-based open requests.
-		}
+		 * @return {@link DomainFile} which corresponds to program open request or null.
-
+		 */
 		public DomainFile getDomainFile() {
 			return domainFile;
 		}
 
-		public int getVersion() {
+		/**
-			return version;
+		 * Get the {@link URL} which corresponds to program open request.  This will be
+		 * null for all non-URL-based open requests.  URL will be a {@link GhidraURL}.
+		 * @return {@link URL} which corresponds to program open request or null.
+		 */
+		public URL getGhidraURL() {
+			return ghidraURL;
 		}
 
+		/**
+		 * Get the {@link URL} which corresponds to the link domainFile used to open a program.
+		 * @return {@link URL} which corresponds to the link domainFile used to open a program.
+		 */
+		public URL getLinkURL() {
+			return linkURL;
+		}
+
+		/**
+		 * Get the open Program instance which corresponds to this open request.
+		 * @return program instance or null if never opened.
+		 */
+		public Program getProgram() {
+			return program;
+		}
+
+		/**
+		 * Release opened program.  This must be done once, and only once, on a successful 
+		 * open request.  If handing ownership off to another consumer, they should be added
+		 * as a program consumer prior to invoking this method.  Releasing the last consumer
+		 * will close the program instance.
+		 */
+		public void release() {
+			if (program != null) {
+				program.release(consumer);
+			}
+		}
+
+		private Program openProgram(DomainFile df, URL url) {
+			if (version != DomainFile.DEFAULT_VERSION) {
+				return (Program) openVersionedFile(df, url, version);
+			}
+			if (forceReadOnly) {
+				return (Program) openReadOnlyFile(df, url, version);
+			}
+			return openUnversionedFile(df);
+		}
+
+		void open() {
+			DomainFile df = domainFile;
+			URL url = ghidraURL;
+			GhidraURLWrappedContent wrappedContent = null;
+			Object content = null;
+			try {
+				if (df == null && url != null) {
+					GhidraURLConnection c = (GhidraURLConnection) url.openConnection();
+					Object obj = c.getContent(); // read-only access
+					if (c.getStatusCode() == StatusCode.UNAUTHORIZED) {
+						return; // assume user already notified
+					}
+					if (!(obj instanceof GhidraURLWrappedContent)) {
+						messageBadProgramURL(url);
+						return;
+					}
+					wrappedContent = (GhidraURLWrappedContent) obj;
+					content = wrappedContent.getContent(this);
+					if (!(content instanceof DomainFile)) {
+						messageBadProgramURL(url);
+						return;
+					}
+					df = (DomainFile) content;
+
+					if (ProgramLinkContentHandler.PROGRAM_LINK_CONTENT_TYPE
+							.equals(df.getContentType())) {
+						Msg.showError(this, null, "Program Multi-Link Error",
+							"Multi-link Program access not supported: " + url);
+						return;
+					}
+				}
+
+				if (!Program.class.isAssignableFrom(df.getDomainObjectClass())) {
+					Msg.showError(this, null, "Error Opening Program",
+						"File does not correspond to a Ghidra Program: " + df.getPathname());
+					return;
+				}
+
+				program = openProgram(df, url);
+
+			}
+			catch (MalformedURLException e) {
+				Msg.showError(this, null, "Invalid Ghidra URL",
+					"Improperly formed Ghidra URL: " + url);
+			}
+			catch (IOException e) {
+				Msg.showError(this, null, "Program Open Failed",
+					"Failed to open Ghidra URL: " + e.getMessage());
+			}
+			finally {
+				if (content != null) {
+					wrappedContent.release(content, this);
+				}
+			}
+
+			if (program != null) {
+				openedProgramList.add(this);
+			}
+		}
+
+		private void messageBadProgramURL(URL url) {
+			Msg.error("Invalid Ghidra URL",
+				"Ghidra URL does not reference a Ghidra Program: " + url);
+		}
 	}
 
 }

Ghidra/Features/Base/src/main/java/ghidra/app/util/viewer/field/Annotation.java

@@ -33,6 +33,7 @@ public class Annotation {
 	private static final Pattern QUOTATION_PATTERN =
 		Pattern.compile("(?<!\\\\)[\"](.*?)(?<!\\\\)[\"]");
 
+	private static List<AnnotatedStringHandler> ANNOTATED_STRING_HANDLERS;
 	private static Map<String, AnnotatedStringHandler> ANNOTATED_STRING_MAP;
 
 	private String annotationText;
@@ -40,6 +41,13 @@ public class Annotation {
 	private AnnotatedStringHandler annotatedStringHandler;
 	private AttributedString displayString;
 
+	public static List<AnnotatedStringHandler> getAnnotatedStringHandlers() {
+		if (ANNOTATED_STRING_HANDLERS == null) {
+			ANNOTATED_STRING_HANDLERS = getSupportedAnnotationHandlers();
+		}
+		return ANNOTATED_STRING_HANDLERS;
+	}
+
 	private static Map<String, AnnotatedStringHandler> getAnnotatedStringHandlerMap() {
 		if (ANNOTATED_STRING_MAP == null) { // lazy init due to our use of ClassSearcher
 			ANNOTATED_STRING_MAP = createAnnotatedStringHandlerMap();
@@ -47,24 +55,28 @@ public class Annotation {
 		return ANNOTATED_STRING_MAP;
 	}
 
-	// locates AnnotatedStringHandler implementations to handle annotations
 	private static Map<String, AnnotatedStringHandler> createAnnotatedStringHandlerMap() {
 		Map<String, AnnotatedStringHandler> map = new HashMap<>();
-
+		for (AnnotatedStringHandler instance : getAnnotatedStringHandlers()) {
-		// find all instances of AnnotatedString
-		List<AnnotatedStringHandler> instances =
-			ClassSearcher.getInstances(AnnotatedStringHandler.class);
-
-		for (AnnotatedStringHandler instance : instances) {
 			String[] supportedAnnotations = instance.getSupportedAnnotations();
 			for (String supportedAnnotation : supportedAnnotations) {
 				map.put(supportedAnnotation, instance);
 			}
 		}
-
 		return Collections.unmodifiableMap(map);
 	}
 
+	// locates AnnotatedStringHandler implementations to handle annotations
+	private static List<AnnotatedStringHandler> getSupportedAnnotationHandlers() {
+		List<AnnotatedStringHandler> list = new ArrayList<>();
+		for (AnnotatedStringHandler h : ClassSearcher.getInstances(AnnotatedStringHandler.class)) {
+			if (h.getSupportedAnnotations().length != 0) {
+				list.add(h);
+			}
+		}
+		return Collections.unmodifiableList(list);
+	}
+
 	/**
 	 * Constructor
 	 * <b>Note</b>: This constructor assumes that the string starts with "{<pre>@</pre>" and ends with '}'
@@ -184,14 +196,6 @@ public class Annotation {
 		return annotationText;
 	}
 
-	public static AnnotatedStringHandler[] getAnnotatedStringHandlers() {
-		Set<AnnotatedStringHandler> annotations =
-			new HashSet<>(getAnnotatedStringHandlerMap().values());
-		AnnotatedStringHandler[] retVal = new AnnotatedStringHandler[annotations.size()];
-		annotations.toArray(retVal);
-		return retVal;
-	}
-
 	/*package*/ static Set<String> getAnnotationNames() {
 		return Collections.unmodifiableSet(getAnnotatedStringHandlerMap().keySet());
 	}

Ghidra/Features/Base/src/main/java/ghidra/app/util/viewer/field/GhidraLocalURLAnnotatedStringHandler.java

@@ -0,0 +1,34 @@
+/* ###
+ * IP: GHIDRA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package ghidra.app.util.viewer.field;
+
+/**
+ * This implementation expands {@link URLAnnotatedStringHandler} providing an example form
+ * of a local project Ghidra URL.
+ */
+public class GhidraLocalURLAnnotatedStringHandler extends URLAnnotatedStringHandler {
+
+	@Override
+	public String getDisplayString() {
+		return "Ghidra-URL(local)";
+	}
+
+	@Override
+	public String getPrototypeString() {
+		return "{@url \"ghidra:/dirpath/myproject?/folder/program.exe#symbol\" \"display string\"}";
+	}
+
+}

Ghidra/Features/Base/src/main/java/ghidra/app/util/viewer/field/GhidraServerURLAnnotatedStringHandler.java

@@ -0,0 +1,34 @@
+/* ###
+ * IP: GHIDRA
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package ghidra.app.util.viewer.field;
+
+/**
+ * This implementation expands {@link URLAnnotatedStringHandler} providing an example form
+ * of a Ghidra Server URL.
+ */
+public class GhidraServerURLAnnotatedStringHandler extends URLAnnotatedStringHandler {
+
+	@Override
+	public String getDisplayString() {
+		return "Ghidra-URL(remote)";
+	}
+
+	@Override
+	public String getPrototypeString() {
+		return "{@url \"ghidra://myserver/myrepo/folder/program.exe#symbol\" \"display string\"}";
+	}
+
+}

Ghidra/Features/Base/src/main/java/ghidra/app/util/viewer/field/URLAnnotatedStringHandler.java

@@ -36,8 +36,10 @@ import ghidra.util.Msg;
  * displayed.
  */
 public class URLAnnotatedStringHandler implements AnnotatedStringHandler {
+
 	private static final String INVALID_SYMBOL_TEXT =
-		"@url annotation must have a URL string " + "optionally followed by a display string";
+		"@url annotation must have a URL string optionally followed by a display string";
+
 	private static final String[] SUPPORTED_ANNOTATIONS = { "url", "hyperlink", "href", "link" };
 
 	@Override

Ghidra/Features/Base/src/main/java/ghidra/base/project/GhidraProject.java

@@ -233,6 +233,13 @@ public class GhidraProject {
 		return project;
 	}
 
+	/**
+	 * Returns the underlying ProjectData instance.
+	 */
+	public ProjectData getProjectData() {
+		return projectData;
+	}
+
 	/**
 	 * Closes the ghidra project, closing (without saving!) any open programs in
 	 * that project. Also deletes the project if created as a temporary project.

Ghidra/Features/Base/src/main/java/ghidra/framework/main/DataTreeDialog.java

@@ -93,7 +93,10 @@ public class DataTreeDialog extends DialogComponentProvider
 	private Integer treeSelectionMode;
 
 	/**
-	 * Construct a new DataTreeDialog.
+	 * Construct a new DataTreeDialog.  This chooser will show all project files.  
+	 * Following linked-folders will only be allowed if a type of {@link #CHOOSE_FOLDER}
+	 * or {@link #OPEN} is specified.  If different behavior is required a filter should 
+	 * be specified using the other constructor. 
 	 *
 	 * @param parent dialog's parent
 	 * @param title title to use
@@ -101,7 +104,7 @@ public class DataTreeDialog extends DialogComponentProvider
 	 * @throws IllegalArgumentException if invalid type is specified
 	 */
 	public DataTreeDialog(Component parent, String title, int type) {
-		this(parent, title, type, null);
+		this(parent, title, type, getDefaultFilter(type));
 	}
 
 	/**
@@ -119,6 +122,20 @@ public class DataTreeDialog extends DialogComponentProvider
 		initDataTreeDialog(type, filter);
 	}
 
+	private static DomainFileFilter getDefaultFilter(int type) {
+		if (type == CHOOSE_FOLDER || type == OPEN) {
+			// return filter which forces folder selection and allow navigation into linked-folders
+			return new DomainFileFilter() {
+
+				@Override
+				public boolean accept(DomainFile df) {
+					return true; // show all files (legacy behavior)
+				}
+			};
+		}
+		return null;
+	}
+
 	public void setTreeSelectionMode(int mode) {
 		if (treePanel != null) {
 			treePanel.getTreeSelectionModel().setSelectionMode(mode);

Ghidra/Features/Base/src/main/java/ghidra/test/TestEnv.java

@@ -18,6 +18,7 @@ package ghidra.test;
 import java.awt.Dialog;
 import java.awt.Window;
 import java.io.*;
+import java.net.URL;
 import java.util.*;
 import java.util.concurrent.atomic.AtomicReference;
 import java.util.stream.Collectors;
@@ -47,6 +48,7 @@ import ghidra.framework.plugintool.Plugin;
 import ghidra.framework.plugintool.PluginTool;
 import ghidra.framework.plugintool.util.PluginException;
 import ghidra.framework.project.DefaultProjectManager;
+import ghidra.framework.protocol.ghidra.GhidraURL;
 import ghidra.program.database.ProgramDB;
 import ghidra.program.model.data.FileDataTypeManager;
 import ghidra.program.model.lang.*;
@@ -874,26 +876,15 @@ public class TestEnv {
 	 * @param domainFile The domain file used to launch the tool; may be null
 	 * @return the tool that is launched
 	 */
-	public PluginTool launchTool(final String toolName, final DomainFile domainFile) {
+	public PluginTool launchTool(String toolName, DomainFile domainFile) {
 		AtomicReference<PluginTool> ref = new AtomicReference<>();
 
 		AbstractGenericTest.runSwing(() -> {
-			boolean wasErrorGUIEnabled = AbstractDockingTest.isUseErrorGUI();
+			PluginTool newTool = doLaunchTool(toolName);
-			AbstractDockingTest.setErrorGUIEnabled(false); // disable the error GUI while launching the tool
-			FrontEndTool frontEndToolInstance = getFrontEndTool();
-
-			Project project = frontEndToolInstance.getProject();
-			ToolServices toolServices = project.getToolServices();
-			PluginTool newTool = toolServices.launchTool(toolName, null);
-			if (newTool == null) {
-				// couldn't find the tool in the workspace...check the test area
-				newTool = launchDefaultToolByName(toolName);
-			}
-
 			ref.set(newTool);
-
+			if (newTool != null) {
-			AbstractDockingTest.setErrorGUIEnabled(wasErrorGUIEnabled);
+				newTool.acceptDomainFiles(new DomainFile[] { domainFile });
-			newTool.acceptDomainFiles(new DomainFile[] { domainFile });
+			}
 		});
 
 		PluginTool launchedTool = ref.get();
@@ -906,6 +897,52 @@ public class TestEnv {
 		return launchedTool;
 	}
 
+	/**
+	 * Launches a tool of the given name using the given Ghidra URL.
+	 * <p>
+	 * Note: the tool returned will have auto save disabled by default.
+	 *
+	 * @param toolName the name of the tool to launch
+	 * @param ghidraUrl The Ghidra URL to be opened in tool (see {@link GhidraURL})
+	 * @return the tool that is launched
+	 */
+	public PluginTool launchToolWithURL(String toolName, URL ghidraUrl) {
+		AtomicReference<PluginTool> ref = new AtomicReference<>();
+
+		AbstractGenericTest.runSwing(() -> {
+			PluginTool newTool = doLaunchTool(toolName);
+			ref.set(newTool);
+			if (newTool != null) {
+				newTool.accept(ghidraUrl);
+			}
+		});
+
+		PluginTool launchedTool = ref.get();
+		if (launchedTool == null) {
+			throw new NullPointerException("Unable to launch the tool: " + toolName);
+		}
+
+		// this will make sure that our tool is closed during disposal
+		extraTools.add(launchedTool);
+		return launchedTool;
+	}
+
+	private PluginTool doLaunchTool(String toolName) {
+		boolean wasErrorGUIEnabled = AbstractDockingTest.isUseErrorGUI();
+		AbstractDockingTest.setErrorGUIEnabled(false); // disable the error GUI while launching the tool
+		FrontEndTool frontEndToolInstance = getFrontEndTool();
+
+		Project project = frontEndToolInstance.getProject();
+		ToolServices toolServices = project.getToolServices();
+		PluginTool newTool = toolServices.launchTool(toolName, null);
+		if (newTool == null) {
+			// couldn't find the tool in the workspace...check the test area
+			newTool = launchDefaultToolByName(toolName);
+		}
+		AbstractDockingTest.setErrorGUIEnabled(wasErrorGUIEnabled);
+		return newTool;
+	}
+
 	/**
 	 * Sets the auto-save feature for all tool instances running under the {@link FrontEndTool}
 	 * created by this TestEnv instance.  Auto-save is off by default when testing.

Ghidra/Features/Base/src/test.slow/java/ghidra/app/util/viewer/field/AnnotationTest.java

@@ -19,6 +19,8 @@ import static org.hamcrest.CoreMatchers.*;
 import static org.junit.Assert.*;
 
 import java.awt.*;
+import java.net.MalformedURLException;
+import java.net.URL;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -37,6 +39,8 @@ import ghidra.framework.model.*;
 import ghidra.framework.plugintool.ServiceProvider;
 import ghidra.framework.plugintool.TestDummyServiceProvider;
 import ghidra.framework.project.ProjectDataService;
+import ghidra.framework.protocol.ghidra.GhidraURLConnection;
+import ghidra.framework.store.FileSystem;
 import ghidra.program.database.ProgramBuilder;
 import ghidra.program.database.ProgramDB;
 import ghidra.program.model.address.Address;
@@ -620,6 +624,60 @@ public class AnnotationTest extends AbstractGhidraHeadedIntegrationTest {
 		assertTrue(spyNavigatable.navigatedTo(otherProgramPath, address));
 	}
 
+	@Test
+	public void testGhidraLocalUrlAnnotation_Program_WithAddress() {
+
+		SpyNavigatable spyNavigatable = new SpyNavigatable();
+		SpyServiceProvider spyServiceProvider = new SpyServiceProvider();
+
+		String addresstring = "1001000";
+
+		String pathname = "/a/b/prog";
+		String url = "ghidra:/folder/project?" + pathname + "#" + addresstring;
+		String annotationText = "{@url \"" + url + "\"}";
+		String rawComment = "My comment - " + annotationText;
+		AttributedString prototype = prototype();
+		FieldElement element =
+			CommentUtils.parseTextForAnnotations(rawComment, program, prototype, 0);
+
+		String displayString = element.getText();
+		assertEquals("My comment - " + url, displayString);
+
+		AnnotatedTextFieldElement annotatedElement = getAnnotatedTextFieldElement(element);
+		click(spyNavigatable, spyServiceProvider, annotatedElement);
+
+		assertTrue(spyServiceProvider.programOpened(pathname));
+
+		// Navigation performed by ProgramManager not tested due to use of spyServiceProvider
+	}
+
+	@Test
+	public void testGhidraServerUrlAnnotation_Program_WithAddress() {
+
+		SpyNavigatable spyNavigatable = new SpyNavigatable();
+		SpyServiceProvider spyServiceProvider = new SpyServiceProvider();
+
+		String addresstring = "1001000";
+
+		String pathname = "/a/b/prog";
+		String url = "ghidra://server/repo" + pathname + "#" + addresstring;
+		String annotationText = "{@url \"" + url + "\"}";
+		String rawComment = "My comment - " + annotationText;
+		AttributedString prototype = prototype();
+		FieldElement element =
+			CommentUtils.parseTextForAnnotations(rawComment, program, prototype, 0);
+
+		String displayString = element.getText();
+		assertEquals("My comment - " + url, displayString);
+
+		AnnotatedTextFieldElement annotatedElement = getAnnotatedTextFieldElement(element);
+		click(spyNavigatable, spyServiceProvider, annotatedElement);
+
+		assertTrue(spyServiceProvider.programOpened(pathname));
+
+		// Navigation performed by ProgramManager not tested due to use of spyServiceProvider
+	}
+
 	@Test
 	public void testUnknownAnnotation() {
 		String rawComment = "This is a symbol {@syyyybol bob} annotation";
@@ -903,13 +961,7 @@ public class AnnotationTest extends AbstractGhidraHeadedIntegrationTest {
 		private Set<String> openedPrograms = new HashSet<>();
 		private Set<String> closedPrograms = new HashSet<>();
 
-		@Override
+		private Program generateProgram(String pathname, String name) {
-		public Program openProgram(DomainFile domainFile, int version, int state) {
-			String name = domainFile.getName();
-			String pathname = domainFile.getPathname();
-
-			openedPrograms.add(name);
-
 			try {
 				ProgramBuilder builder = new ProgramBuilder();
 				builder.setName(pathname);
@@ -923,6 +975,39 @@ public class AnnotationTest extends AbstractGhidraHeadedIntegrationTest {
 			}
 		}
 
+		@Override
+		public Program openProgram(URL ghidraURL, int state) {
+			try {
+				GhidraURLConnection c = new GhidraURLConnection(ghidraURL);
+				String folderpath = c.getFolderPath();
+				String name = c.getFolderItemName();
+				String pathname = folderpath;
+				if (!pathname.endsWith(FileSystem.SEPARATOR)) {
+					pathname += FileSystem.SEPARATOR;
+				}
+				pathname += name;
+				openedPrograms.add(name);
+
+				Program p = generateProgram(pathname, name);
+
+				// NOTE: URL ref navigation not performed
+
+				return p;
+			}
+			catch (MalformedURLException e) {
+				failWithException("Bad URL", e);
+			}
+			return null;
+		}
+
+		@Override
+		public Program openProgram(DomainFile domainFile, int version, int state) {
+			String name = domainFile.getName();
+			String pathname = domainFile.getPathname();
+			openedPrograms.add(name);
+			return generateProgram(pathname, name);
+		}
+
 		@Override
 		public boolean closeProgram(Program p, boolean ignoreChanges) {
 			String name = FilenameUtils.getName(p.getName());

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

@@ -121,12 +121,7 @@ public class ProjectFileManagerTest extends AbstractGhidraHeadedIntegrationTest
 		// If there are queued actions, then we have to kick the handling thread and 
 		// let it finish running.
 
-		try {
+		assertTrue(eventManager.flushEvents(DEFAULT_WAIT_TIMEOUT, TimeUnit.MILLISECONDS));
-			assertTrue(eventManager.flushEvents(DEFAULT_WAIT_TIMEOUT, TimeUnit.MILLISECONDS));
-		}
-		catch (InterruptedException e) {
-			failWithException("Interrupted waiting for filesystem events", e);
-		}
 	}
 
 	private void deleteAll(File file) {

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

@@ -421,15 +421,10 @@ public class DataTreeDialogTest extends AbstractGhidraHeadedIntegrationTest {
 		assertNotNull(dialog);
 	}
 
-	private DomainFileFilter createStartsWithFilter(String startsWith) {
+	private void showFiltered(final String startsWith) {
-		return (df) -> df.getName().startsWith(startsWith);
-	}
-
-	private void showFiltered(String startsWith) {
 		SwingUtilities.invokeLater(() -> {
 			dialog = new DataTreeDialog(frontEndTool.getToolFrame(), "Test Data Tree Dialog",
-				DataTreeDialog.OPEN, createStartsWithFilter(startsWith));
+				DataTreeDialog.OPEN, f -> f.getName().startsWith(startsWith));
-
 			dialog.showComponent();
 		});
 		waitForSwing();

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

@@ -79,10 +79,10 @@ public class AddViewToProjectTest extends AbstractGhidraHeadlessIntegrationTest
 
 		try {
 			URL view = GhidraURL.makeURL(DIRECTORY_NAME, PROJECT_VIEW1);
-			project.addProjectView(view);
+			project.addProjectView(view, true);
 
 			// add another view that will be removed to test the remove
-			project.addProjectView(GhidraURL.makeURL(DIRECTORY_NAME, PROJECT_VIEW2));
+			project.addProjectView(GhidraURL.makeURL(DIRECTORY_NAME, PROJECT_VIEW2), true);
 
 			// validate the view was added to project
 			ProjectLocator[] projViews = project.getProjectViews();

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

@@ -117,7 +117,7 @@ public class CreateDomainObjectTest extends AbstractGhidraHeadedIntegrationTest
 		project.close();
 		Project project2 = ProjectTestUtils.getProject(testDir, PROJECT_NAME2);
 		try {
-			project2.addProjectView(GhidraURL.makeURL(testDir, PROJECT_NAME1));
+			project2.addProjectView(GhidraURL.makeURL(testDir, PROJECT_NAME1), true);
 		}
 		catch (Exception e) {
 			Assert.fail("View Not found");

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

@@ -15,15 +15,18 @@
  */
 package ghidra.base.project;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.HashMap;
 import java.util.Map;
 
-import generic.test.TestUtils;
+import generic.test.AbstractGTest;
 import ghidra.framework.model.DomainFile;
 import ghidra.framework.remote.User;
+import ghidra.framework.store.local.IndexedV1LocalFileSystem;
 import ghidra.framework.store.local.LocalFileSystem;
 import ghidra.test.TestEnv;
+import utilities.util.FileUtilities;
 
 /**
  * This class represents the idea of a shared Ghidra repository.  This class is meant to be
@@ -54,11 +57,34 @@ public class FakeRepository {
 	private Map<String, User> usersByName = new HashMap<>();
 	private Map<User, FakeSharedProject> projectsByUser = new HashMap<>();
 
+	private File versionedFSDir;
 	private LocalFileSystem versionedFileSystem;
 
-	public FakeRepository() {
+	public FakeRepository() throws IOException {
 		// validation must be enabled if both environments are utilized by a test
 		LocalFileSystem.setValidationRequired();
+
+		versionedFSDir =
+			new File(AbstractGTest.getTestDirectoryPath() + File.separator + "TestRepo.rep");
+		if (versionedFSDir.exists()) {
+			FileUtilities.deleteDir(versionedFSDir);
+		}
+		if (versionedFSDir.exists() || !FileUtilities.createDir(versionedFSDir)) {
+			throw new IOException("Failed to create clean repo dir: " + versionedFSDir);
+		}
+		versionedFileSystem = new MyVersionedFileSystem(versionedFSDir.getPath());
+	}
+
+	private static class MyVersionedFileSystem extends IndexedV1LocalFileSystem {
+		MyVersionedFileSystem(String rootPath) throws IOException {
+			super(rootPath, true, false, true, true);
+		}
+
+		@Override
+		public boolean isShared() {
+			// Enables use of asyncronous event dispatching thread
+			return true;
+		}
 	}
 
 	/**
@@ -109,11 +135,6 @@ public class FakeRepository {
 
 		FakeSharedProject project = new FakeSharedProject(this, user);
 		projectsByUser.put(user, project);
-
-		if (versionedFileSystem == null) {
-			versionedFileSystem = project.getVersionedFileSystem();
-			TestUtils.setInstanceField("isShared", versionedFileSystem, Boolean.TRUE);
-		}
 		return project;
 	}
 
@@ -139,6 +160,8 @@ public class FakeRepository {
 	 */
 	public void dispose() {
 		projectsByUser.values().forEach(p -> disposeProject(p));
+		versionedFileSystem.dispose();
+		FileUtilities.deleteDir(versionedFSDir);
 	}
 
 	private void disposeProject(FakeSharedProject p) {

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

@@ -25,7 +25,7 @@ import java.util.concurrent.TimeUnit;
 
 import org.apache.commons.lang3.StringUtils;
 
-import generic.test.AbstractGenericTest;
+import generic.test.AbstractGTest;
 import generic.test.TestUtils;
 import ghidra.framework.data.*;
 import ghidra.framework.model.*;
@@ -39,6 +39,7 @@ import ghidra.test.TestProgramManager;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.task.TaskMonitor;
 import junit.framework.AssertionFailedError;
+import utilities.util.FileUtilities;
 
 /**
  * This class represents the idea of a shared Ghidra project.  Each project is associated with
@@ -61,21 +62,18 @@ public class FakeSharedProject {
 	public FakeSharedProject(FakeRepository repo, User user) throws IOException {
 
 		this.repo = repo;
-		String projectDirPath = AbstractGenericTest.getTestDirectoryPath();
+		String projectDirPath = AbstractGTest.getTestDirectoryPath();
 		gProject =
 			GhidraProject.createProject(projectDirPath, "TestProject_" + user.getName(), true);
 		gProject.setDeleteOnClose(true);
 
-		LocalFileSystem fs = repo.getSharedFileSystem();
+		// use local shared fake repo versioned file system
-		if (fs != null) {
+		setVersionedFileSystem(repo.getSharedFileSystem());
-			// first project will keeps its versioned file system
-			setVersionedFileSystem(fs);
-		}
 	}
 
 	FakeSharedProject(User user) throws IOException {
 
-		String projectDirPath = AbstractGenericTest.getTestDirectoryPath();
+		String projectDirPath = AbstractGTest.getTestDirectoryPath();
 		gProject =
 			GhidraProject.createProject(projectDirPath, "TestProject_" + user.getName(), true);
 	}
@@ -101,7 +99,7 @@ public class FakeSharedProject {
 	 * @return the project file manager
 	 */
 	public ProjectFileManager getProjectFileManager() {
-		return (ProjectFileManager) gProject.getProject().getProjectData();
+		return (ProjectFileManager) gProject.getProjectData();
 	}
 
 	/**
@@ -369,8 +367,11 @@ public class FakeSharedProject {
 	 * @see FakeRepository#dispose()
 	 */
 	public void dispose() {
+		ProjectLocator projectLocator = getProjectFileManager().getProjectLocator();
 		programManager.disposeOpenPrograms();
 		gProject.close();
+		FileUtilities.deleteDir(projectLocator.getProjectDir());
+		projectLocator.getMarkerFile().delete();
 	}
 
 	@Override
@@ -400,12 +401,7 @@ public class FakeSharedProject {
 			(FileSystemEventManager) TestUtils.getInstanceField("eventManager",
 				versionedFileSystem);
 
-		try {
+		eventManager.flushEvents(DEFAULT_WAIT_TIMEOUT, TimeUnit.MILLISECONDS);
-			eventManager.flushEvents(DEFAULT_WAIT_TIMEOUT, TimeUnit.MILLISECONDS);
-		}
-		catch (InterruptedException e) {
-			failWithException("Interrupted waiting for filesystem events", e);
-		}
 	}
 
 	private DomainFolder getFolder(String path) throws Exception {

Ghidra/Features/FunctionID/ghidra_scripts/CollectFailedRelocations.java

@@ -99,6 +99,10 @@ public class CollectFailedRelocations extends GhidraScript {
 			if (monitor.isCancelled()) {
 				return;
 			}
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}

Ghidra/Features/FunctionID/ghidra_scripts/CreateMultipleLibraries.java

@@ -258,6 +258,10 @@ public class CreateMultipleLibraries extends GhidraScript {
 		DomainFile[] files = myFolder.getFiles();
 		for (DomainFile domainFile : files) {
 			monitor.checkCanceled();
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}

Ghidra/Features/FunctionID/ghidra_scripts/FidStatistics.java

@@ -372,6 +372,10 @@ public class FidStatistics extends GhidraScript {
 		DomainFile[] files = folder.getFiles();
 		for (DomainFile domainFile : files) {
 			monitor.checkCanceled();
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}

Ghidra/Features/FunctionID/ghidra_scripts/FindErrors.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.
@@ -17,6 +16,9 @@
 //Opens all programs under a chosen domain folder, grabs their error count,
 //then sorts in increasing error order and prints them
 //@category FunctionID
+import java.io.IOException;
+import java.util.*;
+
 import generic.stl.Pair;
 import ghidra.app.script.GhidraScript;
 import ghidra.framework.model.DomainFile;
@@ -27,9 +29,6 @@ import ghidra.util.Msg;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.VersionException;
 
-import java.io.IOException;
-import java.util.*;
-
 public class FindErrors extends GhidraScript {
 
 	@Override
@@ -82,6 +81,10 @@ public class FindErrors extends GhidraScript {
 			if (monitor.isCancelled()) {
 				return;
 			}
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}

Ghidra/Features/FunctionID/ghidra_scripts/FindFunctionByHash.java

@@ -100,6 +100,10 @@ public class FindFunctionByHash extends GhidraScript {
 			if (monitor.isCancelled()) {
 				return;
 			}
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}

Ghidra/Features/FunctionID/ghidra_scripts/FindNamedFunction.java

@@ -16,6 +16,9 @@
 //Opens all programs under a chosen domain folder, scans them for functions
 //that match a user supplied name, and prints info about the match.
 //@category FunctionID
+import java.io.IOException;
+import java.util.ArrayList;
+
 import ghidra.app.script.GhidraScript;
 import ghidra.feature.fid.service.FidService;
 import ghidra.framework.model.DomainFile;
@@ -26,9 +29,6 @@ import ghidra.util.Msg;
 import ghidra.util.exception.CancelledException;
 import ghidra.util.exception.VersionException;
 
-import java.io.IOException;
-import java.util.ArrayList;
-
 public class FindNamedFunction extends GhidraScript {
 
 	FidService service;
@@ -85,6 +85,10 @@ public class FindNamedFunction extends GhidraScript {
 			if (monitor.isCancelled()) {
 				return;
 			}
+			// Do not follow folder-links or consider program links.  Using content type
+			// to filter is best way to control this.  If program links should be considered
+			// "Program.class.isAssignableFrom(domainFile.getDomainObjectClass())"
+			// should be used.
 			if (domainFile.getContentType().equals(ProgramContentHandler.PROGRAM_CONTENT_TYPE)) {
 				programs.add(domainFile);
 			}