Aj-snapshot is a small program that can be used to make snapshots of the connections made between JACK and/or ALSA clients. 

Since JACK provides both audio and MIDI support to programs, aj-snapshot is able to store both types of connections for JACK. 

Run aj-snapshot in daemon mode to have your connections continually restored.

NOTE:
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You can use either JACK version 1 (default) or 2 (on SlackBuilds.org, JACK v1 is jack-audio-connection-kit and JACK v2 is jack2).