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I propose the following change:
https://github.com/geotools/geotools/pull/402
It allows the z-dimension to be encoded in GML2 whenever it is present in the data (it does now only if the CRS is explicitly 3D). This is already how it works for most of the other output formats such as GML31 and 32.
I have also tested impact on performance, which is not very big:
a postgis table of 1 million polygons, each having 1500 coordinates:
before patch, without z encoding --------------------------------------------- real 21m59.280s user 0m22.649s sys 15m50.355s
after patch, with z ------------------------- real 24m42.808s user 0m36.914s sys 20m10.624
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