diff --git a/src/main/java/hudson/plugins/scm_sync_configuration/SCMManipulator.java b/src/main/java/hudson/plugins/scm_sync_configuration/SCMManipulator.java
index 24de088f..3aafced7 100644
--- a/src/main/java/hudson/plugins/scm_sync_configuration/SCMManipulator.java
+++ b/src/main/java/hudson/plugins/scm_sync_configuration/SCMManipulator.java
@@ -2,6 +2,16 @@
 
 import hudson.plugins.scm_sync_configuration.model.ScmContext;
 import hudson.plugins.scm_sync_configuration.scms.SCM;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Iterator;
+import java.util.List;
+import java.util.logging.Level;
+import java.util.logging.Logger;
+
 import org.apache.maven.scm.ScmException;
 import org.apache.maven.scm.ScmFile;
 import org.apache.maven.scm.ScmFileSet;
@@ -9,6 +19,7 @@
 import org.apache.maven.scm.command.checkin.CheckInScmResult;
 import org.apache.maven.scm.command.checkout.CheckOutScmResult;
 import org.apache.maven.scm.command.remove.RemoveScmResult;
+import org.apache.maven.scm.command.status.StatusScmResult;
 import org.apache.maven.scm.command.update.UpdateScmResult;
 import org.apache.maven.scm.manager.NoSuchScmProviderException;
 import org.apache.maven.scm.manager.ScmManager;
@@ -124,7 +135,17 @@ public List<File> deleteHierarchy(File hierarchyToDelete){
 
         try {
             ScmFileSet deleteFileSet = new ScmFileSet(enclosingDirectory, hierarchyToDelete);
-            RemoveScmResult removeResult = this.scmManager.remove(this.scmRepository, deleteFileSet, "");
+            StatusScmResult checkForChanges = this.scmManager.status(scmRepository, deleteFileSet);
+            LOGGER.fine("Checking for changes on SCM hierarchy ["+hierarchyToDelete.getAbsolutePath()+"] from SCM ...");
+            for (ScmFile changedFile : checkForChanges.getChangedFiles()) {
+                //check in this change as it affect our hierarchy
+                LOGGER.fine("[checkForChanges] Found changed file "+changedFile.toString()+", try to check-in...");
+                CheckInScmResult checkedInChangedFile = scmManager.checkIn(scmRepository, new ScmFileSet(enclosingDirectory.getParentFile(), new File(changedFile.getPath())), "Check-In changes for "+changedFile.getPath());
+                if(!checkedInChangedFile.isSuccess()){
+                  LOGGER.severe("[checkForChanges] Failed to check-in changed file ["+changedFile.getPath()+"]: "+checkedInChangedFile.getProviderMessage());
+              }
+            }
+            RemoveScmResult removeResult = this.scmManager.remove(this.scmRepository, deleteFileSet, "Delete hierarchy "+hierarchyToDelete.getPath());
             if(!removeResult.isSuccess()){
                 LOGGER.severe("[deleteHierarchy] Problem during remove : "+removeResult.getProviderMessage());
                 return null;
diff --git a/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationBusiness.java b/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationBusiness.java
index a2feba7b..4383a35e 100644
--- a/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationBusiness.java
+++ b/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationBusiness.java
@@ -39,6 +39,7 @@ public class ScmSyncConfigurationBusiness {
     private SCMManipulator scmManipulator;
     private File checkoutScmDirectory = null;
     private ScmSyncConfigurationStatusManager scmSyncConfigurationStatusManager = null;
+    private List<String> manualSynchronizationIncludes = new ArrayList<String>();
 
     /**
      * Use of a size 1 thread pool frees us from worrying about accidental thread death and
@@ -187,8 +188,17 @@ private void processCommitsQueue() {
                             String firstNonExistingParentScmPath = pathRelativeToJenkinsRoot.getFirstNonExistingParentScmPath();
 
                             try {
-                                FileUtils.copyDirectory(JenkinsFilesHelper.buildFileFromPathRelativeToHudsonRoot(pathRelativeToJenkinsRoot.getPath()),
-                                        fileTranslatedInScm);
+                                File buildFileFromPathRelativeToHudsonRoot = JenkinsFilesHelper.buildFileFromPathRelativeToHudsonRoot(pathRelativeToJenkinsRoot.getPath());
+                                FileUtils.copyDirectory(buildFileFromPathRelativeToHudsonRoot, fileTranslatedInScm, new FileFilter() {
+                                  @Override
+                                  public boolean accept(File pathname) {
+                                    if(pathname.getPath().endsWith(".xml") 
+                                        || getManualSynchronizationIncludes().contains(pathname)){
+                                      return true;
+                                    }
+                                    return false;
+                                  }
+                                });
                             } catch (IOException e) {
                                 throw new LoggableException("Error while copying file hierarchy to SCM directory", FileUtils.class, "copyDirectory", e);
                             }
@@ -212,7 +222,8 @@ private void processCommitsQueue() {
                 }
                 for(Path path : commit.getChangeset().getPathsToDelete()){
                     List<File> deletedFiles = deleteHierarchy(commit.getScmContext(), path);
-                    updatedFiles.addAll(deletedFiles);
+                    if(deletedFiles != null)
+                      updatedFiles.addAll(deletedFiles);
                 }
 
                 if(updatedFiles.isEmpty()){
@@ -245,6 +256,15 @@ private void processCommitsQueue() {
         }
     }
 
+    public List<String> getManualSynchronizationIncludes() {
+      return manualSynchronizationIncludes;
+    }
+
+    public void setManualSynchronizationIncludes(
+        List<String> manualSynchronizationIncludes) {
+      this.manualSynchronizationIncludes = manualSynchronizationIncludes;
+    }
+
     private boolean writeScmContentOnlyIfItDiffers(Path pathRelativeToJenkinsRoot, byte[] content, File fileTranslatedInScm)
             throws LoggableException {
         boolean scmContentUpdated = false;
diff --git a/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationPlugin.java b/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationPlugin.java
index ef1b7da9..12774461 100644
--- a/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationPlugin.java
+++ b/src/main/java/hudson/plugins/scm_sync_configuration/ScmSyncConfigurationPlugin.java
@@ -164,7 +164,8 @@ public void loadData(ScmSyncConfigurationPOJO pojo){
         this.displayStatus = pojo.isDisplayStatus();
         this.commitMessagePattern = pojo.getCommitMessagePattern();
         this.manualSynchronizationIncludes = pojo.getManualSynchronizationIncludes();
-    }
+        this.business.setManualSynchronizationIncludes(manualSynchronizationIncludes);
+	}
 
     protected void initialInit() throws Exception {
         // We need to init() here in addition to ScmSyncConfigurationItemListener.onLoaded() to ensure that we do
@@ -227,6 +228,8 @@ public void configure(StaplerRequest req, JSONObject formData)
         } else {
             this.manualSynchronizationIncludes = new ArrayList<String>();
         }
+        
+        this.business.setManualSynchronizationIncludes(manualSynchronizationIncludes);
 
         // Repo initialization should be made _before_ plugin save, in order to let scm-sync-configuration.xml
         // file synchronizable
diff --git a/src/main/java/hudson/plugins/scm_sync_configuration/model/ChangeSet.java b/src/main/java/hudson/plugins/scm_sync_configuration/model/ChangeSet.java
index d2927b29..7514f3ac 100644
--- a/src/main/java/hudson/plugins/scm_sync_configuration/model/ChangeSet.java
+++ b/src/main/java/hudson/plugins/scm_sync_configuration/model/ChangeSet.java
@@ -75,7 +75,7 @@ public Map<Path, byte[]> getPathContents(){
         for(Path pathToAdd : filteredPathContents.keySet()){
             for(Path pathToDelete : pathsToDelete){
                 // Removing paths being both in pathsToDelete and pathContents
-                if(pathToDelete.contains(pathToAdd)){
+                if(pathToDelete.equals(pathToAdd)){
                     filteredPaths.add(pathToAdd);
                 }
             }