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And after all that, editing (simply rotating) the photo in different applications has different results. Some change only the Orientation tag, others change the actual data, some seem to change both so it's still incorrect when opened in other viewers; and then there's the embedded thumbnail (but that is rarely used), so the result is a mess.

I'm interested in your PhotoStructure application, just subscribed to the beta!

When you rotate a photo or video in PhotoStructure, you can have it persist rotation/orientation by updating the file directly (PhotoStructure uses exiftool under the hood), but it's not the default out of concern for unknown bugs that may invalidate the original file in some way.

By default it just writes the new orientation to an XMP or MIE sidecar. The downside of this approach is that most applications don't respect sidecars.

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