diff --git a/build.gradle b/build.gradle
index a47a85356..ef06b11d4 100644
--- a/build.gradle
+++ b/build.gradle
@@ -191,6 +191,10 @@ dependencies {
 
     implementation group: 'com.beust', name: 'jcommander', version: '1.72'
 
+    // jsoup HTML parser library @ https://jsoup.org/
+    implementation group: 'org.jsoup', name: 'jsoup', version: '1.17.2'
+
+
     // Test Dependencies
     //testImplementation 'junit:junit:4.11'
     testImplementation group: 'org.gradle', name: 'gradle-core', version: '6.1.1'
@@ -225,10 +229,13 @@ dependencies {
     distribution group: 'org.openjfx', name: 'javafx-fxml', version: '11.0.2', classifier: 'win'
     distribution group: 'org.openjfx', name: 'javafx-controls', version: '11.0.2', classifier: 'win'
     distribution group: 'org.openjfx', name: 'javafx-swing', version: '11.0.2', classifier: 'win'
+    distribution group: 'org.openjfx', name: 'javafx-graphics', version: '11.0.2', classifier: 'win'
+    distribution group: 'org.openjfx', name: 'javafx-base', version: '11.0.2', classifier: 'win'
     distribution group: 'org.openjfx', name: 'javafx-fxml', version: '11.0.2', classifier: 'mac'
     distribution group: 'org.openjfx', name: 'javafx-controls', version: '11.0.2', classifier: 'mac'
     distribution group: 'org.openjfx', name: 'javafx-swing', version: '11.0.2', classifier: 'mac'
-
+    distribution group: 'org.openjfx', name: 'javafx-graphics', version: '11.0.2', classifier: 'mac'
+    distribution group: 'org.openjfx', name: 'javafx-base', version: '11.0.2', classifier: 'mac'
 
     // This ensures classpath load order to match the MagicDraw provided order and then includes extras needed for non-OpenAPI stuff.
     // This was necessary because of the Application class stubbing that was done in the chromium libraries.
@@ -292,7 +299,7 @@ task extractDependencies {
                     from 'build/dependency-cache/extracted/magicdraw/plugins/com.nomagic.conceptmodeler'
                     into 'build/tmp/com.nomagic.conceptmodeler'
                 }
-                
+
             }
         }
         fileTree(dir: 'build/dependency-cache/extracted/magicdraw', include: '*.zip').each { archive ->
@@ -300,7 +307,7 @@ task extractDependencies {
                 from zipTree(archive)
                 into 'build/dependency-cache/extracted/magicdraw'
             }
-            
+
         }
         delete 'build/dependency-cache/extracted/magicdraw/plugins/com.nomagic.conceptmodeler'
     }
@@ -579,7 +586,7 @@ nexusPublishing {
 
 artifactoryPublish {
     publications('mavenJava')
-    
+
 }
 
 artifactoryPublish.dependsOn distZip
diff --git a/gradle.properties b/gradle.properties
index 8ab140a8d..11290532f 100644
--- a/gradle.properties
+++ b/gradle.properties
@@ -1,4 +1,4 @@
-version=6.1.0
+version=6.1.1
 group=org.openmbee.mdk.magic
 descriptorFile=MDR_Plugin_Model_Development_Kit_91110_descriptor.xml
 magicdDrawGroupName=org.openmbee.mdk
diff --git a/src/main/java/org/openmbee/mdk/api/incubating/MDKConstants.java b/src/main/java/org/openmbee/mdk/api/incubating/MDKConstants.java
index 9e6d07081..9ede7bd57 100644
--- a/src/main/java/org/openmbee/mdk/api/incubating/MDKConstants.java
+++ b/src/main/java/org/openmbee/mdk/api/incubating/MDKConstants.java
@@ -74,6 +74,7 @@ public class MDKConstants {
             MESSAGES_NODE = "messages",
             REJECTED_NODE = "rejected",
             SOURCE_FIELD = "source",
+            ARCHIVED_FIELD = "_archived",
             DELETED_FIELD = "deleted",
             MAGICDRAW_SOURCE_VALUE = "magicdraw",
             ELEMENT_TYPE_VALUE = "Element",
diff --git a/src/main/java/org/openmbee/mdk/emf/EMFExporter.java b/src/main/java/org/openmbee/mdk/emf/EMFExporter.java
index 0b59794eb..95fa73359 100644
--- a/src/main/java/org/openmbee/mdk/emf/EMFExporter.java
+++ b/src/main/java/org/openmbee/mdk/emf/EMFExporter.java
@@ -25,11 +25,15 @@
 import org.openmbee.mdk.json.JacksonUtils;
 import org.openmbee.mdk.util.MDUtils;
 import org.openmbee.mdk.util.Utils;
+import org.w3c.dom.html.HTMLDocument;
 import org.eclipse.emf.ecore.EDataType;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.EReference;
 import org.eclipse.emf.ecore.EStructuralFeature;
 import org.eclipse.emf.ecore.util.EcoreUtil;
+import org.jsoup.Jsoup;
+import org.jsoup.nodes.Document;
+import org.jsoup.select.Elements;
 
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
@@ -39,6 +43,7 @@
 import java.util.function.BiFunction;
 import java.util.stream.Collectors;
 import java.io.Reader;
+import java.io.StringReader;
 
 public class EMFExporter implements BiFunction<Element, Project, ObjectNode> {
     @Override
@@ -161,7 +166,13 @@ private enum Processor {
         DOCUMENTATION_PRE(
                 (element, project, objectNode) -> {
                     //Todo: FIgure out how to read this stuff and parse the <a tags from MD
-                    // String doc_text = (String) Utils.getElementAttribute(element, Utils.AvailableAttribute.Documentation);
+                    String doc_text = (String) Utils.getElementAttribute(element, Utils.AvailableAttribute.Documentation);
+                    Document doc = Jsoup.parse(doc_text);
+                    Elements crossReferences = doc.select("a[href^=mdel:]");
+                    if (!crossReferences.isEmpty()) {
+                        crossReferences.tagName("mms-cf");
+                        
+                    }
                     // Reader reader = new StringReader(doc_text);
                     // HTMLDocument html = new HTMLDocument(doc_text);
                     objectNode.put(MDKConstants.DOCUMENTATION_KEY, (String) Utils.getElementAttribute(element, Utils.AvailableAttribute.Documentation));
diff --git a/src/main/java/org/openmbee/mdk/mms/actions/ValidateBranchesAction.java b/src/main/java/org/openmbee/mdk/mms/actions/ValidateBranchesAction.java
index d2e1cbc78..3c585a0f3 100644
--- a/src/main/java/org/openmbee/mdk/mms/actions/ValidateBranchesAction.java
+++ b/src/main/java/org/openmbee/mdk/mms/actions/ValidateBranchesAction.java
@@ -20,8 +20,8 @@ public class ValidationRunner implements RunnableWithProgress {
 
         @Override
         public void run(ProgressStatus arg0) {
-            BranchValidator branchValidator = new BranchValidator(Application.getInstance().getProject());
-            branchValidator.validate(arg0, true);
+            BranchValidator branchValidator = new BranchValidator(Application.getInstance().getProject(), true);
+            branchValidator.run(arg0);
             if (branchValidator.hasErrors()) {
                 Application.getInstance().getGUILog().log("[ERROR] Unable to complete validate branches action.");
                 return;
diff --git a/src/main/java/org/openmbee/mdk/mms/sync/delta/DeltaSyncRunner.java b/src/main/java/org/openmbee/mdk/mms/sync/delta/DeltaSyncRunner.java
index 8e57e7edf..31046fed5 100644
--- a/src/main/java/org/openmbee/mdk/mms/sync/delta/DeltaSyncRunner.java
+++ b/src/main/java/org/openmbee/mdk/mms/sync/delta/DeltaSyncRunner.java
@@ -12,6 +12,7 @@
 import com.nomagic.magicdraw.openapi.uml.SessionManager;
 import com.nomagic.task.ProgressStatus;
 import com.nomagic.task.RunnableWithProgress;
+import com.nomagic.ui.ProgressStatusRunner;
 import com.nomagic.uml2.ext.magicdraw.classes.mdkernel.Element;
 import com.nomagic.uml2.ext.magicdraw.classes.mdkernel.ValueSpecification;
 import org.openmbee.mdk.api.incubating.MDKConstants;
@@ -59,12 +60,16 @@ public DeltaSyncRunner(boolean shouldCommit, boolean shouldCommitDeletes, boolea
         this.shouldCommit = shouldCommit;
         this.shouldCommitDeletes = shouldCommitDeletes;
         this.shouldUpdate = shouldUpdate;
-    }
-
+    }   
+    
     @SuppressWarnings("unchecked")
     @Override
     public void run(ProgressStatus progressStatus) {
-        progressStatus.setDescription("Initializing");
+        progressStatus.setDescription("Coordinated Sync: Initializing");
+        progressStatus.setCurrent(0);
+        progressStatus.setIndeterminate(false);
+        progressStatus.setMax(15);
+        progressStatus.cancelIfCanceled();
         if (ProjectUtilities.isFromEsiServer(project.getPrimaryProject()) && EsiUtils.getLoggedUserName() == null) {
             Utils.guilog("[WARNING] You need to be logged in to Teamwork Cloud first. Skipping sync. All changes will be persisted in the model and re-attempted in the next sync.");
             return;
@@ -78,9 +83,13 @@ public void run(ProgressStatus progressStatus) {
             Utils.guilog("[ERROR] An error occurred while validating credentials. Credentials will be cleared. Skipping sync. All changes will be persisted in the model and re-attempted in the next sync. Reason: " + e.getMessage());
             return;
         }
+        progressStatus.increase();
+        progressStatus.setDescription("Coordinated Sync: Project Validation");
+        progressStatus.cancelIfCanceled();
 
         ProjectValidator pv = new ProjectValidator(project);
-        pv.validate();
+        ProgressStatusRunner.runWithProgressStatus(pv, "Coordinated Sync: Project Validation", true, 0);
+
         if (pv.hasErrors()) {
             Application.getInstance().getGUILog().log("[WARNING] Coordinated Sync can not complete and will be skipped.");
             return;
@@ -90,9 +99,12 @@ public void run(ProgressStatus progressStatus) {
             Utils.displayValidationWindow(project, pv.getValidationSuite(), "Coordinated Sync Pre-Condition Validation");
             return;
         }
-
-        BranchValidator bv = new BranchValidator(project);
-        bv.validate(null, false);
+        progressStatus.increase();
+        progressStatus.setDescription("Coordinated Sync: Branch Validation");
+        progressStatus.cancelIfCanceled();
+        
+        BranchValidator bv = new BranchValidator(project, false);
+        ProgressStatusRunner.runWithProgressStatus(bv, "Coordinated Sync: Branch Validation", true, 0);
         if (bv.hasErrors()) {
             Application.getInstance().getGUILog().log("[WARNING] Coordinated sync can not complete and will be skipped.");
             return;
@@ -102,7 +114,7 @@ public void run(ProgressStatus progressStatus) {
             Utils.displayValidationWindow(project, bv.getValidationSuite(), "Coordinated Sync Pre-Condition Validation");
             return;
         }
-
+        progressStatus.increase();
         LocalDeltaTransactionCommitListener listener = LocalDeltaProjectEventListenerAdapter.getProjectMapping(project).getLocalDeltaTransactionCommitListener();
 
         // UPDATE LOCKS
@@ -110,7 +122,8 @@ public void run(ProgressStatus progressStatus) {
         listener.setDisabled(true);
 
         // UPDATE MMS CHANGELOG
-
+        progressStatus.setDescription("Coordinated Sync: Updating Server Changelog");
+        progressStatus.cancelIfCanceled();
         try {
             if (!MMSDeltaProjectEventListenerAdapter.getProjectMapping(project).update()) {
                 Application.getInstance().getGUILog().log("[WARNING] MMS history is unavailable. Skipping sync. All changes will be re-attempted in the next sync.");
@@ -121,9 +134,10 @@ public void run(ProgressStatus progressStatus) {
             e.printStackTrace();
             return;
         }
-
+        progressStatus.increase();
         // BUILD COMPLETE LOCAL CHANGELOG
-
+        progressStatus.setDescription("Coordinated Sync: Building Local Changelog");
+        progressStatus.cancelIfCanceled();
         Changelog<String, Element> persistedLocalChangelog = new Changelog<>();
         Collection<SyncElement> persistedLocalSyncElements = SyncElements.getAllByType(project, SyncElement.Type.LOCAL);
         for (SyncElement syncElement : persistedLocalSyncElements) {
@@ -154,8 +168,10 @@ else if (value instanceof Element) {
                 localUpdated = localChangelog.get(Changelog.ChangeType.UPDATED),
                 localDeleted = localChangelog.get(Changelog.ChangeType.DELETED);
 
+        progressStatus.increase();
         // BUILD COMPLETE MMS CHANGELOG
-
+        progressStatus.setDescription("Coordinated Sync: Building Server Changelog");
+        progressStatus.cancelIfCanceled();
         Changelog<String, Void> persistedMmsChangelog = new Changelog<>();
         Collection<SyncElement> persistedMmsSyncElements = SyncElements.getAllByType(project, SyncElement.Type.MMS);
         for (SyncElement syncElement : persistedMmsSyncElements) {
@@ -177,9 +193,9 @@ else if (value instanceof Element) {
         Map<String, ObjectNode> mmsJsons = new HashMap<>(elementIdsToGet.size());
 
         // Get latest json for element added/changed from MMS
-
+        progressStatus.increase();
         if (!elementIdsToGet.isEmpty()) {
-            progressStatus.setDescription("Getting " + elementIdsToGet.size() + " added/changed element" + (elementIdsToGet.size() != 1 ? "s" : "") + " from MMS");
+            progressStatus.setDescription("Coordinated Sync: Getting " + elementIdsToGet.size() + " added/changed element" + (elementIdsToGet.size() != 1 ? "s" : "") + " from MMS");
             File responseFile;
             ObjectNode response;
             try {
@@ -220,8 +236,8 @@ else if (value instanceof Element) {
         }
 
         // NEW CONFLICT DETECTION
-
-        progressStatus.setDescription("Detecting conflicts");
+        progressStatus.increase();
+        progressStatus.setDescription("Coordinated Sync: Detecting conflicts");
         Map<String, Pair<Changelog.Change<Element>, Changelog.Change<Void>>> conflictedChanges = new LinkedHashMap<>(),
                 unconflictedChanges = new LinkedHashMap<>();
         localChangelog.findConflicts(mmsChangelog, (change, change2) -> change != null && change2 != null, conflictedChanges, unconflictedChanges);
@@ -305,13 +321,13 @@ else if (shouldUpdate && mmsChange != null) {
         }
 
         // POINT OF NO RETURN
-
+        progressStatus.increase();
         // COMMIT UNCONFLICTED CREATIONS AND UPDATES TO MMS
         String projectId = Converters.getIProjectToIdConverter().apply(project.getPrimaryProject());
         String refId = MDUtils.getBranchId(project);
         boolean shouldLogNoLocalChanges = shouldCommit;
         if (shouldCommit && !localElementsToPost.isEmpty()) {
-            progressStatus.setDescription("Committing creations and updates to MMS");
+            progressStatus.setDescription("Coordinated Sync: Committing creations and updates to MMS");
             LinkedList<ObjectNode> postElements = new LinkedList<>();
             for (Element element : localElementsToPost.values()) {
                 ObjectNode elementObjectNode = Converters.getElementToJsonConverter().apply(element, project);
@@ -345,12 +361,12 @@ else if (shouldUpdate && mmsChange != null) {
                 shouldLogNoLocalChanges = false;
             }
         }
-
+        progressStatus.increase();
         // COMMIT UNCONFLICTED DELETIONS TO MMS
         // NEEDS TO BE AFTER LOCAL; EX: MOVE ELEMENT OUT ON MMS, DELETE OWNER LOCALLY, WHAT HAPPENS?
 
         if (shouldCommit && shouldCommitDeletes && !deleteElements.isEmpty()) {
-            progressStatus.setDescription("Committing deletions to MMS");
+            progressStatus.setDescription("Coordinated Sync: Committing deletions to MMS");
             try {
                 File file = MMSUtils.createEntityFile(this.getClass(), ContentType.APPLICATION_JSON, deleteElements, MMSUtils.JsonBlobType.ELEMENT_ID);
                 HttpRequestBase elementsDeleteRequest = MMSUtils.prepareEndpointBuilderBasicJsonDeleteRequest(MMSElementsEndpoint.builder(), project, file)
@@ -373,7 +389,7 @@ else if (shouldUpdate && mmsChange != null) {
         }
 
         // OUTPUT RESULT OF LOCAL CHANGES
-
+        progressStatus.increase();
         if (shouldLogNoLocalChanges) {
             Application.getInstance().getGUILog().log("[INFO] No local changes to commit to MMS.");
         }
@@ -381,7 +397,7 @@ else if (shouldUpdate && mmsChange != null) {
         // ADD CREATED ELEMENTS LOCALLY FROM MMS
         // CHANGE UPDATED ELEMENTS LOCALLY FROM MMS
         // REMOVE DELETED ELEMENTS LOCALLY FROM MMS
-
+        progressStatus.increase();
         if (shouldUpdate) {
             listener.setDisabled(true);
 
@@ -401,8 +417,8 @@ else if (shouldUpdate && mmsChange != null) {
         }
 
         // HANDLE CONFLICTS
-
-        progressStatus.setDescription("Finishing up");
+        progressStatus.increase();
+        progressStatus.setDescription("Coordinated Sync: Finishing up");
 
         Set<Element> localConflictedElements = new HashSet<>();
         Set<ObjectNode> mmsConflictedElements = new HashSet<>();
@@ -422,7 +438,7 @@ else if (shouldUpdate && mmsChange != null) {
         }
 
         ElementValidator elementValidator = new ElementValidator("CSync Conflict Validation", ElementValidator.buildElementPairs(localConflictedElements, project), mmsConflictedElements, project);
-        elementValidator.run(progressStatus);
+        ProgressStatusRunner.runWithProgressStatus(elementValidator, "Element Validation", true, 0);
         if (!elementValidator.getInvalidElements().isEmpty()) {
             Application.getInstance().getGUILog().log("[INFO] There are potential conflicts in " + elementValidator.getInvalidElements().size() + " element" + (elementValidator.getInvalidElements().size() != 1 ? "s" : "") + " between MMS and local changes. Please resolve them and re-sync.");
             vss.add(elementValidator.getValidationSuite());
@@ -447,7 +463,7 @@ else if (shouldUpdate && mmsChange != null) {
         }
 
         // CLEAR IN-MEMORY AND PERSIST UNPROCESSED & FAILURES
-
+        progressStatus.increase();
         listener.setDisabled(true);
         Project project = Application.getInstance().getProject();
         if (!SessionManager.getInstance().isSessionCreated(project)) {
@@ -502,7 +518,7 @@ else if (shouldUpdate && mmsChange != null) {
 
         SessionManager.getInstance().closeSession(project);
         listener.setDisabled(false);
-
+        progressStatus.increase();
         // SUCCESS
         failure = false;
     }
diff --git a/src/main/java/org/openmbee/mdk/mms/sync/manual/ManualSyncRunner.java b/src/main/java/org/openmbee/mdk/mms/sync/manual/ManualSyncRunner.java
index 3dd32ebce..66132186d 100644
--- a/src/main/java/org/openmbee/mdk/mms/sync/manual/ManualSyncRunner.java
+++ b/src/main/java/org/openmbee/mdk/mms/sync/manual/ManualSyncRunner.java
@@ -53,7 +53,8 @@ public void run(ProgressStatus progressStatus) {
         progressStatus.setIndeterminate(true);
 
         ProjectValidator pv = new ProjectValidator(project);
-        pv.validate();
+        
+        pv.run(progressStatus);
         if (pv.hasErrors()) {
             Application.getInstance().getGUILog().log("[ERROR] Project validation could not be completed. Manual validation aborted.");
             return;
@@ -64,8 +65,8 @@ public void run(ProgressStatus progressStatus) {
         }
 
         if (project.isRemote()) {
-            BranchValidator bv = new BranchValidator(project);
-            bv.validate(null, false);
+            BranchValidator bv = new BranchValidator(project, false);
+            bv.run(null);
             if (bv.hasErrors()) {
                 Application.getInstance().getGUILog().log("[ERROR] Branch validation could not be completed. Manual validation aborted.");
                 return;
diff --git a/src/main/java/org/openmbee/mdk/mms/validation/BranchValidator.java b/src/main/java/org/openmbee/mdk/mms/validation/BranchValidator.java
index e59d84562..0ee4f0fd0 100644
--- a/src/main/java/org/openmbee/mdk/mms/validation/BranchValidator.java
+++ b/src/main/java/org/openmbee/mdk/mms/validation/BranchValidator.java
@@ -13,6 +13,8 @@
 import com.nomagic.magicdraw.core.project.ProjectDescriptorsFactory;
 import com.nomagic.magicdraw.esi.EsiUtils;
 import com.nomagic.task.ProgressStatus;
+import com.nomagic.task.RunnableWithProgress;
+
 import org.openmbee.mdk.actions.ClipboardAction;
 import org.openmbee.mdk.api.incubating.MDKConstants;
 import org.openmbee.mdk.api.incubating.convert.Converters;
@@ -39,9 +41,10 @@
 import java.text.NumberFormat;
 import java.util.*;
 
-public class BranchValidator {
+public class BranchValidator implements RunnableWithProgress {
 
     private final Project project;
+    private boolean allBranches;
     private boolean errors;
     private ValidationSuite validationSuite = new ValidationSuite("structure");
     //    private ValidationRule twcMissingBranchValidationRule = new ValidationRule("Missing in Client", "Branch shall exist in TWC if it exists in MMS.", ViolationSeverity.WARNING);
@@ -49,15 +52,16 @@ public class BranchValidator {
     private ValidationRule branchEquivalenceValidationRule = new ValidationRule("Branch Equivalence", "Branch shall be represented in MagicDraw and MMS equivalently.", ViolationSeverity.ERROR);
     private ValidationRule mmsBuildingBranchValidationRule = new ValidationRule("Building on Server", "Branch shall be completely built on MMS before it is used.", ViolationSeverity.WARNING);
 
-    public BranchValidator(Project project) {
+    public BranchValidator(Project project, boolean allBranches) {
         this.project = project;
+        this.allBranches = allBranches;
 //        validationSuite.addValidationRule(twcMissingBranchValidationRule);
         validationSuite.addValidationRule(mmsMissingBranchValidationRule);
         validationSuite.addValidationRule(branchEquivalenceValidationRule);
         validationSuite.addValidationRule(mmsBuildingBranchValidationRule);
     }
 
-    public void validate(ProgressStatus progressStatus, boolean allBranches) {
+    public void run(ProgressStatus progressStatus) {
         if (project == null) {
             return;
         }
@@ -82,7 +86,7 @@ public void validate(ProgressStatus progressStatus, boolean allBranches) {
         }
 
         Collection<EsiUtils.EsiBranchInfo> targetBranches = null;
-        if (allBranches) {
+        if (this.allBranches) {
             try {
                 ProjectDescriptor projectDescriptor = ProjectDescriptorsFactory.createAnyRemoteProjectDescriptor(project);
                 targetBranches = EsiUtils.getBranches(projectDescriptor);
@@ -107,7 +111,7 @@ public void validate(ProgressStatus progressStatus, boolean allBranches) {
             String entryKey;
             if ((value = branchJson.get(MDKConstants.ID_KEY)) != null && value.isTextual()) {
                 entryKey = value.asText();
-                if (allBranches || entryKey.equals(currentBranch)) {
+                if (this.allBranches || entryKey.equals(currentBranch)) {
                     clientBranches.put(entryKey, new Pair<>(branch, branchJson));
                 }
             }
@@ -135,7 +139,7 @@ public void validate(ProgressStatus progressStatus, boolean allBranches) {
                         String entryKey;
                         if ((value = refObjectNode.get(MDKConstants.ID_KEY)) != null && value.isTextual()) {
                             entryKey = value.asText();
-                            if (allBranches || entryKey.equals(currentBranch)) {
+                            if (this.allBranches || entryKey.equals(currentBranch)) {
                                 serverBranches.put(entryKey, refObjectNode);
                             }
                         }
@@ -186,7 +190,11 @@ else if (serverBranch == null) {
                 serverBranch.remove(MDKConstants.STATUS_KEY);
                 serverBranch.remove(MDKConstants.PARENT_COMMIT_ID);
 
-                clientBranch.getValue().put(MDKConstants.DELETED_FIELD, false);
+                clientBranch.getValue().put(MDKConstants.ARCHIVED_FIELD, false);
+                if (serverBranch.get(MDKConstants.DELETED_FIELD) != null) {
+                    serverBranch.set(MDKConstants.ARCHIVED_FIELD, serverBranch.get(MDKConstants.DELETED_FIELD));
+                    serverBranch.remove(MDKConstants.DELETED_FIELD);
+                }
                 JsonNode diff = JsonPatchFunction.getInstance().apply(clientBranch.getValue(), serverBranch);
                 if (diff != null && diff.isArray() && diff.size() > 0) {
                     ValidationRuleViolation v = new ValidationRuleViolation(project.getPrimaryModel(), "[BRANCH NOT EQUIVALENT] The Teamwork Cloud branch \"" + clientBranch.getKey().getName() + "\" is not equivalent to the corresponding MMS branch.");
diff --git a/src/main/java/org/openmbee/mdk/mms/validation/ProjectValidator.java b/src/main/java/org/openmbee/mdk/mms/validation/ProjectValidator.java
index 951059a1b..979522b77 100644
--- a/src/main/java/org/openmbee/mdk/mms/validation/ProjectValidator.java
+++ b/src/main/java/org/openmbee/mdk/mms/validation/ProjectValidator.java
@@ -9,7 +9,8 @@
 import com.nomagic.magicdraw.core.ProjectUtilities;
 import com.nomagic.magicdraw.esi.EsiUtils;
 import com.nomagic.magicdraw.esi.EsiUtils.EsiBranchInfo;
-
+import com.nomagic.task.ProgressStatus;
+import com.nomagic.task.RunnableWithProgress;
 import com.nomagic.magicdraw.teamwork2.ITeamworkService;
 import com.nomagic.magicdraw.teamwork2.TeamworkService;
 import org.openmbee.mdk.api.incubating.MDKConstants;
@@ -25,7 +26,8 @@
 import org.openmbee.mdk.validation.ViolationSeverity;
 import org.apache.http.client.methods.HttpRequestBase;
 import org.apache.http.entity.ContentType;
-import org.openmbee.mdk.mms.endpoints.MMSProjectsEndpoint;
+import org.openmbee.mdk.mms.endpoints.MMSProjectEndpoint;
+import org.openmbee.mdk.mms.endpoints.MMSEndpointBuilderConstants;
 
 import javax.swing.JOptionPane;
 import java.io.File;
@@ -56,7 +58,7 @@
  */
 
 
-public class ProjectValidator {
+public class ProjectValidator implements RunnableWithProgress {
 
     private final Project project;
     private boolean errors;
@@ -102,7 +104,8 @@ public void updateTWCServiceToProject(JsonNode projectJson) {
                     MMSUtils.JsonBlobType.PROJECT);
             // generate project post request
             HttpRequestBase request = MMSUtils
-                    .prepareEndpointBuilderBasicJsonPostRequest(MMSProjectsEndpoint.builder(), project, sendData)
+                    .prepareEndpointBuilderBasicJsonPostRequest(MMSProjectEndpoint.builder(), project, sendData)
+                    .addParam(MMSEndpointBuilderConstants.URI_PROJECT_SUFFIX, Converters.getIProjectToIdConverter().apply(project.getPrimaryProject()))
                     .build();
             // do project post request
             MMSUtils.sendMMSRequest(project, request);
@@ -130,13 +133,20 @@ public void checkIfTWCServiceChanged(JsonNode projectJson) {
         }
     }
 
-    public void validate() {
+    @Override
+    public void run(ProgressStatus progressStatus) {
         ObjectNode response;
 
 
         try {
-            HttpRequestBase projectsRequest = MMSUtils.prepareEndpointBuilderBasicGet(MMSProjectsEndpoint.builder(), project).build();
-            File responseFile = MMSUtils.sendMMSRequest(project, projectsRequest);
+            HttpRequestBase projectRequest = MMSUtils.prepareEndpointBuilderBasicGet(MMSProjectEndpoint.builder(), project)
+                    .addParam(MMSEndpointBuilderConstants.URI_PROJECT_SUFFIX, Converters.getIProjectToIdConverter().apply(project.getPrimaryProject()))
+                    .build();
+            if (progressStatus != null) {
+                progressStatus.setDescription("Retrieving Project(s)");
+                progressStatus.setIndeterminate(true);
+            }
+            File responseFile = MMSUtils.sendMMSRequest(project, projectRequest);
             try (JsonParser jsonParser = JacksonUtils.getJsonFactory().createParser(responseFile)) {
                 response = JacksonUtils.parseJsonObject(jsonParser);
             }
diff --git a/src/main/java/org/openmbee/mdk/util/MDUtils.java b/src/main/java/org/openmbee/mdk/util/MDUtils.java
index eaa6fcd75..d4d4a159b 100644
--- a/src/main/java/org/openmbee/mdk/util/MDUtils.java
+++ b/src/main/java/org/openmbee/mdk/util/MDUtils.java
@@ -1,6 +1,5 @@
 package org.openmbee.mdk.util;
 
-import com.nomagic.log.LoggerBridge;
 import com.nomagic.magicdraw.core.Application;
 import com.nomagic.magicdraw.core.Project;
 import com.nomagic.magicdraw.core.ProjectUtilities;
@@ -10,7 +9,6 @@
 import com.nomagic.magicdraw.ui.browser.BrowserTabTree;
 import com.nomagic.magicdraw.ui.browser.Node;
 import com.nomagic.magicdraw.uml.BaseElement;
-import com.nomagic.magicdraw.uml.symbols.DiagramPaintContext;
 import com.nomagic.magicdraw.uml.symbols.DiagramPresentationElement;
 import com.nomagic.magicdraw.uml.symbols.PresentationElement;
 import com.nomagic.uml2.ext.magicdraw.auxiliaryconstructs.mdmodels.Model;
@@ -18,24 +16,15 @@
 import com.nomagic.uml2.ext.magicdraw.classes.mdkernel.Slot;
 import com.nomagic.uml2.ext.magicdraw.classes.mdkernel.TaggedValue;
 import com.nomagic.uml2.ext.magicdraw.classes.mdkernel.ValueSpecification;
-import com.nomagic.utils.CameoUtilities;
-import com.nomagic.utils.FileHelper;
 
 import org.openmbee.mdk.api.incubating.MDKConstants;
 import org.openmbee.mdk.api.incubating.convert.Converters;
 import org.openmbee.mdk.docgen.DocGenUtils;
-import org.apache.batik.anim.dom.SAXSVGDocumentFactory;
-import org.apache.batik.util.XMLResourceDescriptor;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.util.EcoreUtil;
-import org.w3c.dom.Document;
 
 import javax.annotation.CheckForNull;
-import javax.xml.transform.Transformer;
 import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
 import java.awt.event.ActionEvent;
 import java.io.*;
 import java.nio.charset.Charset;
@@ -44,8 +33,6 @@
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import static com.nomagic.magicdraw.uml.DiagramTypeConstants.*;
-
 /**
  * A collection of utility functions for accessing the MagicDraw (MD)
  * application.