- Attached to this report are 4 packages with the following contents:
- PackageA_V1:
-- PackageA/GameObjectA.1.prefab
-- PackageA/GameObjectA.2.prefab
-- PackageShared/GameObjectShared.1.prefab
-- PackageShared/GameObjectShared.2.prefab

- PackageA_V2:
-- PackageA/GameObjectA.1.prefab

- PackageB_V1:
-- PackageB/GameObjectB.1.prefab
-- PackageB/GameObjectB.2.prefab
-- PackageShared/GameObjectShared.1.prefab
-- PackageShared/GameObjectShared.2.prefab

- PackageB_V2:
-- PackageB/GameObjectB.1.prefab
-- PackageB/GameObjectB.2.prefab
-- PackageShared/GameObject.Shared.1.prefab

How to reproduce:

1. Open a new project
2. Import PackageA_V1
- It gets imported properly
3. Import PackageB_V1
- It gets imported, however it's not clear if PackageB metadata is stored separately for the contents of the PackageShared folder
4. Import PackageA_V2
- The default option is to "Re-install Package", which installs a new version of GameObjectA.1.prefab
- Unity does not recognise that certain files and folders were deleted in this package (and does not delete any files)
- It also cannot tell if PackageShared files were added via PackageA or PackageB
5. Import PackageB_V2
- Unity states that there is nothing to import from this package, as all assets are already in this project
- This is not optimal behaviour, as these are potentially completely new files
- End file result:
-- PackageA/GameObjectA.1.prefab from PackageA_V2
-- PackageA/GameObjectA.2.prefab from PackageA_V1
-- PackageB/GameObjectB.1.prefab from PackageB_V1
-- PackageB/GameObjectB.2.prefab from PackageB_V1
-- PackageShared/GameObjectShared.1.prefab from PackageA_V1 or PackageB_V1 (it is not immediately clear which one)
-- PackageShared/GameObjectShared.2.prefab from PackageA_V1 or PackageB_V1 (it is not immediately clear which one)
- Reproduced in Version 5.4.0b1 (3137382c8e08)
- New package import feature

- Won't fix: This feature is now in legacy mode and will be replaced in the future by a new packages manager system. The behaviour described in this bug is a result of current implementation design. To fix this issue would require a rewrite/redesign of the current implementation. We will instead focus our energy on the new system and make sure this bug does not present itself.