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Open Gazebo, resize and reposition the window the way you want it to look when you open it, then on the top menu, choose:

File -> Save Configuration

The next time you open Gazebo, it will open that way ;)

Behind the scenes, Gazebo is updating the ~/.gazebo/gui.ini file with geometry information like this:

[geometry]
width=1330
height=865
x=1148
y=418

You can also change these values manually if you'd like.