Geany itself does not set cursors, I think they are set by the GTK theme, which
is why I suggested the .gtkrc file but I don't know if it can set them there.
Geany will build and run with GTK3 on Linux and (I think) on OSX but it is not
built with GTK3 on windows because nobody has contributed the changes to make
Travis windows build, the nightly windows build and the release build use GTK3,
but if you have the capability you could try building geany with GTK3 and
report back about this and any other problems you encounter.
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