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Notes -
Mavlink always outputs what it calls "MSL" in EGM96 (and it's not correct to refer to HAE as MSL, so that's reasonable), right? The normal ublox protocol that a lot of gps modules use doesn't seem to include the geoid nor the HAE, rather it outputs both MSL and geoid separation (which if it follows NMEA is positive -- height of geoid above ellipsoid). I expect best practice there would be to calculate the HAE and then re-apply whatever geoid model you want to use.
So, the problem I've run into with partners in industry, and you'll see this in the github issue I linked, they read the GPS_RAW_INT.alt_ellipsoid field, thinking it's the height above the WGS84 ellipsoid. It is not. It's the height above the EGM96 geoid. MAVLINK does not consider this a bug. It results in a lot of confusion over and over and over again with people insisting adamantly that they are providing the "raw WGS84 height above ellipsoid from the GPS unit".
I keep that github link handy to escape the endless cycle of "But it's the alt_ellipsoid field!" Which is understandable. If I were reading a field called alt_ellipsoid I'd assume it was the altitude over the ellipsoid as well. This is usually caught when they are 100' off a known ground level.
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