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Sublime - Default To Opening In New Window

CLI

You can open something in a new window by adding the -n or --new-window parameter. You could make an alias for this so you don't have to remember.

Nautilus

Open the /usr/share/applications/sublime_text.desktop file:

sudo subl --new-window /usr/share/applications/sublime_text.desktop

Find the execution line and add the -n parameter. E.g.

Exec=/opt/sublime_text/sublime_text --n

References