diff --git a/Tools/XcodeCapp/TNXCodeCapp.h b/Tools/XcodeCapp/TNXCodeCapp.h
index bc61a04dd..b43cfa130 100644
--- a/Tools/XcodeCapp/TNXCodeCapp.h
+++ b/Tools/XcodeCapp/TNXCodeCapp.h
@@ -42,7 +42,6 @@ extern NSString * const XCCListeningStartNotification;
     NSString                        *profilePath;
     NSString                        *PBXModifierScriptPath;
     NSURL                           *currentProjectURL;
-    NSURL                           *XCodeSupportFolder;
     NSURL                           *XCodeSupportProject;
     NSURL                           *XCodeSupportProjectSources;
     PRHEmptyGrowlDelegate           *growlDelegateRef;
diff --git a/Tools/XcodeCapp/TNXCodeCapp.m b/Tools/XcodeCapp/TNXCodeCapp.m
index b2a561e2d..eb90ce76e 100644
--- a/Tools/XcodeCapp/TNXCodeCapp.m
+++ b/Tools/XcodeCapp/TNXCodeCapp.m
@@ -349,11 +349,13 @@ NSString * const XCCListeningStartNotification = @"XCCListeningStartNotification
                         @"",nil];
 
         PBXArguments = [NSArray arrayWithObjects: @"-c",
-                        [NSString stringWithFormat:@"(%@; python %@ add '%@' '%@') 2>&1",
+                        [NSString stringWithFormat:@"(%@; python %@ add '%@' '%@' '%@' '%@') 2>&1",
                          profilePath,
                          PBXModifierScriptPath,
                          XCodeSupportPBXPath,
-                         shadowPath],nil];
+                         shadowPath,
+                         fullPath,
+                         [currentProjectURL path]],nil];
 
         successTitle = @"Objective-J source processed";
         successMsg = splitPath;
@@ -420,11 +422,13 @@ NSString * const XCCListeningStartNotification = @"XCCListeningStartNotification
         NSString *shadowPath = [[self shadowURLForSourceURL:[NSURL URLWithString:[fullPath stringByAddingPercentEscapesUsingEncoding:NSUTF8StringEncoding]]] path];
 
         NSArray *PBXArguments = [NSArray arrayWithObjects: @"-c",
-                        [NSString stringWithFormat:@"(%@; python %@ remove '%@' '%@') 2>&1",
+                        [NSString stringWithFormat:@"(%@; python %@ remove '%@' '%@' '%@' '%@') 2>&1",
                          profilePath,
                          PBXModifierScriptPath,
                          XCodeSupportPBXPath,
-                         shadowPath],nil];
+                         shadowPath,
+                         fullPath,
+                         [currentProjectURL path]],nil];
 
         DLog(@"Removing shadow file: %@", shadowPath);
         [fm removeItemAtPath:shadowPath error:nil];
@@ -484,14 +488,14 @@ NSString * const XCCListeningStartNotification = @"XCCListeningStartNotification
 {
     XCodeSupportProjectName    = [NSString stringWithFormat:@"%@.xcodeproj/", currentProjectName];
     XCodeTemplatePBXPath       = [[NSBundle mainBundle] pathForResource:@"project.pbxproj" ofType:@"sample"];
-    XCodeSupportFolder         = currentProjectURL;
-    XCodeSupportProject        = [NSURL URLWithString:XCodeSupportProjectName relativeToURL:XCodeSupportFolder];
-    XCodeSupportProjectSources = [NSURL URLWithString:@".XcodeSupport/" relativeToURL:XCodeSupportFolder];
+    XCodeSupportProject        = [NSURL URLWithString:XCodeSupportProjectName relativeToURL:currentProjectURL];
+    XCodeSupportProjectSources = [NSURL URLWithString:@".XcodeSupport/" relativeToURL:currentProjectURL];
     XCodeSupportPBXPath        = [NSString stringWithFormat:@"%@/project.pbxproj", [XCodeSupportProject path]];
     PBXModifierScriptPath      = [[NSBundle mainBundle] pathForResource:@"pbxprojModifier" ofType:@"py"];
 
     
-    //[fm removeItemAtURL:XCodeSupportFolder error:nil];
+    //[fm removeItemAtURL:XCodeSupportProjectSources error:nil];
+    //[fm removeItemAtURL:XCodeSupportProject error:nil];
     
     // create the template project if it doesn't exist
     if (![fm fileExistsAtPath:[XCodeSupportProjectSources path]])
@@ -748,11 +752,13 @@ NSString * const XCCListeningStartNotification = @"XCCListeningStartNotification
             [fm removeItemAtPath:shadowFullPath error:nil];
 
             NSArray *PBXArguments = [NSArray arrayWithObjects: @"-c",
-                                     [NSString stringWithFormat:@"(%@; python %@ remove '%@' '%@') 2>&1",
+                                     [NSString stringWithFormat:@"(%@; python %@ remove '%@' '%@' '%@' '%@') 2>&1",
                                       profilePath,
                                       PBXModifierScriptPath,
                                       XCodeSupportPBXPath,
-                                      shadowFullPath],nil];
+                                      shadowFullPath,
+                                      unshadowed,
+                                      [currentProjectURL path]],nil];
 
             DLog(@"Cleaning PBX reference task...");
             NSArray *statusInfo = [self runTask:PBXArguments];
diff --git a/Tools/XcodeCapp/pbxprojModifier.py b/Tools/XcodeCapp/pbxprojModifier.py
index 515c2b860..01141b0bb 100755
--- a/Tools/XcodeCapp/pbxprojModifier.py
+++ b/Tools/XcodeCapp/pbxprojModifier.py
@@ -1,47 +1,42 @@
 import sys, os
 from mod_pbxproj import XcodeProject
 
+XCODESUPPORTFOLDER = ".XcodeSupport"
 
-def add_file(PBXProjectFilePath, path):
+def add_file(project, shadowGroup, sourceGroup, shadowPath, sourcePath, projectBaseURL):
+    project.add_file(shadowPath, parent=shadowGroup)
+    project.add_file(sourcePath, parent=sourceGroup)
+    project.save()
 
-    project = XcodeProject.Load(PBXProjectFilePath)
-    shadowGroup = project.get_or_create_group('Shadows')
-
-    files = project.get_files_by_os_path("XcodeSupport/%s" % os.path.basename(path))
-    
-    if "main.m" in path:
-        sys.exit(0)
-    
-    if len(files) == 0:
-        project.add_file(path, parent=shadowGroup)
-        project.save()
-
-def remove_file(PBXProjectFilePath, path):
-    
-    project = XcodeProject.Load(PBXProjectFilePath)
-    shadowGroup = project.get_or_create_group('Shadows')
-    
-    files = project.get_files_by_os_path("XcodeSupport/%s" % os.path.basename(path))
-    
-    if "main.m" in path:
-        sys.exit(0)
-    
-    if len(files) == 1:
-        project.remove_file("XcodeSupport/%s" % os.path.basename(path), parent=shadowGroup)
-        project.save()
+def remove_file(project, shadowGroup, sourceGroup, shadowPath, sourcePath, projectBaseURL):
+    project.remove_file("%s/%s" % (XCODESUPPORTFOLDER, os.path.basename(shadowPath)), parent=shadowGroup)
+    project.remove_file(os.path.relpath(sourcePath, projectBaseURL), parent=sourceGroup)
+    project.save()
 
 
 if __name__ == '__main__':
 
     action              = sys.argv[1]
     PBXProjectFilePath  = sys.argv[2]
-    currentFilePath     = sys.argv[3]
+    shadowFilePath      = sys.argv[3]
+    sourceFilePath      = sys.argv[4]
+    projectBaseURL      = sys.argv[5]
     
-    if action == "add":
-        add_file(PBXProjectFilePath, currentFilePath)
-    elif action == "remove":
-        remove_file(PBXProjectFilePath, currentFilePath)
+    project = XcodeProject.Load(PBXProjectFilePath)
     
+    shadowGroup = project.get_or_create_group('Shadows')
+    sourceGroup = project.get_or_create_group('Sources')
+    
+    if "main.m" in shadowFilePath:
+        sys.exit(0)
+    
+    files = project.get_files_by_os_path("%s/%s" % (XCODESUPPORTFOLDER, os.path.basename(shadowFilePath)))
+
+    if action == "add" and len(files) == 0:
+        add_file(project, shadowGroup, sourceGroup, shadowFilePath, sourceFilePath, projectBaseURL)
+
+    elif action == "remove" and len(files) == 1:
+        remove_file(project, shadowGroup, sourceGroup, shadowFilePath, sourceFilePath, projectBaseURL)