netCDF files with data ordered from upper left to lower right causes display/interrogation issues.
If the data in a netCDF file is ordered from upper right to lower left GeoServer/GeoTools will display it correctly at an extent which fully encompasses the data. However, interrogation of the data is incorrect and appears to index into the data as if it was ordered from lower left to upper right despite the definitions of the data (points are flipped vertically). Similarly, sub-samples of the netCDF file act in a similar fashion. For example, zooming in to an extent smaller than the dataset and panning vertically redraws the image moving in the wrong direction (panning up, image moves down & vice versa). It appears the code does not respect the data ordering in these two cases.
Attached is a zip containing a sample netCDF file and configuration files (based on the GeoServer curl examples) to reproduce the issue.
Workaround: Reorder data to be ordered LL to UR.