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They can still sit with a notification icon, but now that icon will be in the lower right corner, not shown at all times unless you put the mouse over there.
But more importantly, it doesn't need such an icon anymore. Since there is no "window list" (aka "taskbar") anymore, the "better" way to do this in GNOME Shell is to not have a tray icon; instead, simply put transmission onto its own workspace. Since you can have as many workspaces as you want (they are dynamic and automatic after all), you can afford to do so.
Then when you want to call that transmission instance, just hit the Win (or alt+F1) key or the upper-left hotcorner to call the activities view, type "tr"+enter to switch directly to it (or click the transmission icon that shows up on the dash ("dock") on the left).
Same goes for IM clients like empathy: no need to worry about minimizing them anymore.





Member since:
2005-07-23
Long story short, in Win95 MS introduced the notification area (aka "tray icons") but did not strictly restrict it to system notifications.
Every damn app maker on the planet started abusing it and docking his apps into it.
Microsoft then tried to cover the problem in Windows XP and subsequent releases by making icons autohide in that area... which is a band-aid, not a fix, and a stupid one.
GNOME Shell makes this distinction clear and doesn't allow apps to show icons into the upper right corner, which is reserved for system stuff.