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In fact, the jackd auto-start is a jackd option feature. Yes, it uses the ~/.jackdrc which is conveniently written by qjackctl everytime you start jackd through it. This ~/.jackdrc file contains the exact command line that should be invoked when auto-starting jackd, so its mechanics are very straight forward.

Basic settings for starting jackd under Qtractor control is in the MTDL (Mighty TODO List:).

About the assignable I/O issue. I reckon your wishes to make things easier or user-friendlier. However I'm having some difficulty in realizing those wishes ;) all jack/alsa-seq applications are accessible through the connections dialog (the one cloned from qjackctl;) so how can I make it even easier without making some kind of hardwire to some special application (eg. qsynth, qsampler) ? Maybe I'm just being too stubborn and missing the question in point here. Would you elaborate on that? :)

Cheers
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rncbc aka Rui Nuno Capela