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You should compute the NDWI first then georeference it. This is because NDWI is a ratio, and the linear combination of ratio is not the same as the ratio of the linear combination. You therefore reduce the risk of having artefacts by resampling after computing the NDWI (the resampling will smooth the NDWI a little bit, except if you use a nearest neighbour ...
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The georeference Plugin is a core plugin and can't be deinstalled (just de-activated). You find the plugin (after activation) in the menu raster:
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