The objects have fake users, print(bpy.data.objects['Cube.001'].use_fake_user)

IIRC there is no way to enable this via the UI, though it could have been done via Python. we could change this P324, though its not a very common open for objects.

ah, ok. But then still even if I link obj to scene, and then do:
bpy.data.objects['Cube'].use_fake_user=False

And delete 'Cube' with X key, it is not deleted from group.
Now I just tested this on older blender builds (with fake_user=False), and:

• deleting works ok on another PC -where no testbuild was installed (meaning object is deleted from group, when use_fake_user=False).
• on PC where I installed testbuild 2.77 deletion won't work even on old builds. But I'm sure It worked before installing testbuild 1. So somehow testbuild broke my script even on older blender... Only using 'user_clear' on yellow cubes works-cubes are deleted permanently from group, but there was no need for this trick before testbuild.

ps. I think there is not need for UI for fake_users, because this is mostly usefull for python scripting.

I think I found the reason for buggy behavior.
Basically I blend file below we have red and yellow objects:

• yellow object is member of 'NotWorking' group
• red object is member of 'Working' group.

The only difference is - yellow object is linked to scene when script, from text editor, is executed (this time I set fake_users to False).
So in theory both yellow and red object should have 2 users (bpy.context.object.users): first user is group and second is scene. But red object has only single user, even though he is member of 'Working' group and scene (2 users).
I guess this is why deleting -bpy.ops.object.delete()- red object has different result, from deleting yellow object.
Maybe delete operator should force number of users to be 0 (bpy.context.object.user_clear()), so that object is deleted correctly from group too?

Blend file with slightly modified script (fake users set to false, and it prints number of users of red and yellow objects)

Thanks for quick bug fix :)
However I liked how bpy.ops.object.delete() worked previously (unlinking from scene, and group at same time) :( . I mean for most applications, when user deletes something - it is gone. It was unexpected for me (and I'm sure for other users too), that after deleting object, it was still present as group member, that it why I reported it as bug.
So maybe those three operations could be split in future : unlinking from group, from scene, deletion (unlinking from everything). But I guess this should be reported as new task, right?

Yes, I see how previous behavior kinda looked OK… But imho it was not - e.g. if you linked a same object in several scenes, then what would you expect? that it gets removed from its groups only when you have deleted it from all scenes? that pressing X would immediately remove it from all scenes and groups altogether? Those are more like design decisions…

Point is, 2.77 fixes that inconsistency (we had similar ones with e.g. images when used by ImageEditor and texture, etc.), and now has a consistent behavior. If we want to also remove objects from their group when deleting them from all scenes, then this has to be implemented on the operator level. Think a lot of issues here also comes form the fact that user cannot actually manage object datablock itself (you only have access to it through its instantiations, either directly by scenes, or indirectly through groups). But that’s no bug. ;)

Yep, I totally agree this bug had to be fixed. But I was thinking about 'operator level' design change, as you described it. So the change would be:

• change current bpy.ops.object.delete -> to bpy.ops.object.unlink (because this is what delete operator is currently doing)
• bpy.ops.object.delete - would be new operator now -> completely deleting object from scene, groups etc. It would behave as delete operation in other apps,
• bpy.ops.group.objects_remove(group='xxx') - no change here. This operator does what is says, unlike delete operator IMO.

English is not my native language, so maybe it wasn't clear, but this is what I was thinking about in previous post.
I have already overrode x-key with new 'real' delete operator in python, so I'm happy now :). But I'm thinking, that maybe you could implement this change in blender source code, so other users could benefit from it.