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re. Qjackctl from 2011-11-03 (and using the inbuilt interface to jack session)
ok. and are you using the versioning option when saving/replacing a jack-session?

meanwhile, i'm considering adding the option you request but with a slight twist: this will come in the form of a new user preference, where he/she can chose the default session file format, between regular session format (.qtr or .qts file suffix) and the zip/archive bundle format (.qtz)

this new option applies when saving as usual (File/Save, Save As... menus) and, more important to the subject at hand, to the session file format carried out on a jack-session context to "Save" or "Save and Quit" commands, which currently is the later (.qtz zip/archive bundle) by hard coded default.

however, i have this creepy feeling that having it to a regular session file format (.qtr or .qts) which does not bundle media content at all but just the path references to the external audio/midi files, may bring a lot more trouble than any of the scenario you (long) exposed.

for example, just by having any of the audio/midi files under the jack-session folder or directory, either by accident or by naive mistake, will cause you to potentially loose that precious data or at least making it unreachable later, even though you have qjackctl jack-session versioning enabled. you'll have to pick those files by hand on the file-system and move them to the new jack-session folder. otoh, if you have versioning disabled then you're dead in the water, those files will be lost forever as sson as you save/replace to the same jack-session folder.

cheers