Minimize to tray
Since PB is a reference application you are likely to leave running in the background or relaunch many times during the day, i find it strange that PB doesn´t use the traybar - especially because PB takes some time to launch.
This would make the autorun on startup option much more useful since PB could just load in the background without actually oppening the brain file and throwing the main window at the user. The brain window is then oppened by clicking at the tray icon. From here it should also be possible to right click and choose a different brain file from history.
There should be an option to specify when PB should minimize to tray: on minimize or on close (as many applications have).
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jroeterd commented
With auto-hide every time you set the focus on another windows it gets hidden. This makes it very unnatural to switch between applications.
It is not a big thing but I think it would be relative easy to add "Minimize to tray" to the 'Float' and 'Auto-hide' options.
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BobLytle commented
Have you tried the "Auto-Hide" feature? I typically auto-hide all day long, which reduces the Brain to a circle icon at the right of my screen. The benefit of this vs. tray-ing: I can drag files onto the circle, and up pops the brain for quick dropping. When I click away, it reduces back to the icon. Settings are retained on shutdown, so tomorrow's session starts with auto-hide.