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This is a paid asset, but now you can download UniMerge Free.

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UniMerge v1.11 (Latest version)

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UniMerge v1.7.5

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Having trouble working on Unity assets (scenes and prefabs) as a team? Text-based merge tools not cutting it for scenes and prefabs? Looking for a merge/diff tool in Unity? We have the answer!
Introducing UniMerge: an editor extension visually for merging GameObjects!

Confused? Check out our demo!
Update: I gave a talk about UniMerge at Unite!
UniMerge provides a friendly visual interface for interactively merging hugely complex scenes or scene objects.
Color Coded Differences: Objects that are different are highlighted red for visual merging. The background changes to green instantly once conflict is resolved.
Filter Component Types: Only care about one type of component? Filter out the rest and exclude them from the comparison.
Intelligent Reference Copy: References maintained when copying from one object to the other.
Isolate Differences: At the press of a button, the tool will expand all objects containing differences.
Scene Settings Compare: The Scene Merge window will show a list of editable Render settings, Lightmap settings, NavMesh bake settings, etc. with copy arrows to compare between scenes
New! Large Scene Support: Tested on scenes of up to 50,000 objects!

Check out the full documentation on the Unify wiki.

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