There are a few things that cannot be upgraded at the current time, so we need to warn you about it.
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AGSJoy plugin: Attempts to build your game with this plugin active will not compile with AGS 4 because its Joystick struct will conflict with the AGS own Joystick struct. The solution is to either disable the newest script API level (by lowering it to v3.6.1, but that will also disable anything else), or adjust the code to work with the new Joystick API. The API is relatively simple, so upgrading should not be a huge problem. The plugin is no longer needed after that.
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Speech Center and Translations: Speech Center with translations will stop working with this AGS 4 update. It won't crash, but it won't see translated strings. This is because Translation storage had changed in the Editor. The plugin will have to be updated to work with AGS 4.