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Is MightyBake Unity the same as the stand-alone version?
The two versions of MightyBake share the same core renderer but have different UIs. Some features are available in one before being available in the other. The intention is that they share the same baking functionality, but Unity is able to load meshes directly into the baker while the stand-alone only reads them from files.
Unity uses a left-handed co-ordinate system and MightyBake uses a right handed one.