Rigify now generates the rig into the same armature every time, so you don't have to re-hook-up things like armature modifiers, parenting, etc.

By default the generated rig object is named "rig".  But you can add a custom "rig_object_name" property to the metarig to specify the name of the object to generate into.

release/scripts/modules/rigify/__init__.py

@@ -154,6 +154,8 @@ def generate_rig(context, obj_orig, prefix="ORG-", META_DEF=True):
     from collections import OrderedDict
     import rigify_utils
     reload(rigify_utils)
+    
+    print("Begin...")
 
     # Not needed but catches any errors before duplicating
     validate_rig(context, obj_orig)
@@ -164,23 +166,85 @@ def generate_rig(context, obj_orig, prefix="ORG-", META_DEF=True):
     rest_backup = obj_orig.data.pose_position
     obj_orig.data.pose_position = 'REST'
 
-
     bpy.ops.object.mode_set(mode='OBJECT')
 
     scene = context.scene
 
-    # copy object and data
+    # Check if the generated rig already exists, so we can
+    # regenerate in the same object.  If not, create a new
+    # object to generate the rig in.
+    print("Fetch rig.")
+    try:
+        name = obj_orig["rig_object_name"]
+    except KeyError:
+        name = "rig"
+        
+    try:
+        obj = scene.objects[name]
+    except KeyError:
+        obj = bpy.data.objects.new(name, type='ARMATURE')
+        obj.data = bpy.data.armatures.new(name)
+        scene.objects.link(obj)
+        
+    obj.data.pose_position = 'POSE'
+    
+    # Get rid of anim data in case the rig already existed
+    print("Clear rig animation data.")
+    obj.animation_data_clear()
+        
+    # Select generated rig object
     obj_orig.selected = False
-    obj = obj_orig.copy()
-    obj.data = obj_orig.data.copy()
-    scene.objects.link(obj)
-    scene.objects.active = obj
     obj.selected = True
-
+    scene.objects.active = obj
+    
+    # Remove all bones from the generated rig armature.
+    bpy.ops.object.mode_set(mode='EDIT')
+    for bone in obj.data.edit_bones:
+        obj.data.edit_bones.remove(bone)
+    bpy.ops.object.mode_set(mode='OBJECT')
+    
+    # Create temporary duplicates for merging
+    temp_rig_1 = obj_orig.copy()
+    temp_rig_1.data = obj_orig.data.copy()
+    scene.objects.link(temp_rig_1)
+    
+    temp_rig_2 = obj_orig.copy()
+    temp_rig_2.data = obj.data
+    scene.objects.link(temp_rig_2)
+    
+    # Select the temp rigs for merging
+    for objt in scene.objects:
+        objt.selected = False # deselect all objects
+    temp_rig_1.selected = True
+    temp_rig_2.selected = True
+    scene.objects.active = temp_rig_2
+    
+    # Merge the temporary rigs
+    bpy.ops.object.join(context)
+    
+    # Delete the second temp rig
+    bpy.ops.object.delete()
+    
+    # Select the generated rig
+    for objt in scene.objects:
+        objt.selected = False # deselect all objects
+    obj.selected = True
+    scene.objects.active = obj
+    
+    # Copy over the pose_bone custom properties
+    for bone in obj_orig.pose.bones:
+        for prop in bone.keys():
+            obj.pose.bones[bone.name][prop] = bone[prop]
+    
+    # Create proxy deformation rig
+    # TODO: remove this
     if META_DEF:
         obj_def = obj_orig.copy()
         obj_def.data = obj_orig.data.copy()
         scene.objects.link(obj_def)
+    
+    scene.update()
+    print("On to the real work.")
 
     arm = obj.data
 
@@ -255,7 +319,7 @@ def generate_rig(context, obj_orig, prefix="ORG-", META_DEF=True):
     # for pbone in obj.pose.bones:
     for pbone in bones_sorted:
         bone_name = pbone.name
-
+        print(bone_name)
         if bone_name not in bone_typeinfos:
             continue
 
@@ -268,6 +332,7 @@ def generate_rig(context, obj_orig, prefix="ORG-", META_DEF=True):
         bone_names_pre = {bone.name for bone in arm.bones}
 
         for type_name, type_func in bone_typeinfos[bone_name]:
+            print("    " + type_name)
             # this bones definition of the current typeinfo
             definition = bone_def_dict[type_name]
             options = get_bone_type_options(pbone, type_name)
@@ -386,7 +451,10 @@ def generate_rig(context, obj_orig, prefix="ORG-", META_DEF=True):
     bpy.ops.object.mode_set(mode=mode_orig)
     obj_orig.data.pose_position = rest_backup
     obj.data.pose_position = 'POSE'
+    obj_orig.data.pose_position = 'POSE'
     context.user_preferences.edit.global_undo = global_undo
+    
+    print("Done.\n")
 
     return obj