Suggestions on program layout and storage of Cocoa program that analyzes?

If your software on the iPhone is supposed to run continuously in the background processing data from BTstack, I recommend to create a LaunchDaemon for the data processing and provide a regular app for the configuration. (Although BTstack Mouse / Keyboard / GPS don't follow this advice, they will when I get around to update them - Celeste uses a daemon for the actual file transfers e.g.).

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