Many of these are well documented in the existing tutorials or topics:
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how to write formulas in detail with examples: https://www.youtube.com/watch?v=D4lSjLfPVwY
Most of these things are documented in the many resources about SNAP: -
mask raster layers with water or clouds masks with map algebra (raster calculator) formulas: https://www.youtube.com/watch?v=mIOYXbMouq4
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cropping / clipping a raster by polygon: SNAP: Clip Raster by Shapefile
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getting the minumum bounding geometry of raster layers as polygon: can be retrieved by the collocation tool (page 15-17 here), vector export is currently not possible in SNAP
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extract by mask raster layers using polygon and operations such as intersection of polygon
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supervised classification (maximum likelihood, etc): https://www.youtube.com/watch?v=cUbSYSHexDw
Please let us know if you search for something specific.