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if the the user saves multiple "snapshots" of a session and changes the content of a MIDI clip in one of them, this change will be reflected in all snapshots. Is this the desired behaviour?

yes, it's the expected behavior alright: when taking snapshots in the xml/regular/default session file formats (*.qtr, *.qts) all audio/MIDI files are one and the same as they're external references or paths to the file-system.

however, if the snapshots are saved as a zip/archive session file format (*.qtz) then each one will bundle its own version of the audio/MIDI files, as each e get a compressed copy in each zip-archive snapshot.

hth.
cheers