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I want to let a timer run to wait for a scene change, but the problem is that when i pause the whole tree it simply just completely freezes everything and nothing works.
I expect the timer to be the reason, because he is also in the tree.
By default, the pause mode of nodes is set to inherit, so all nodes mimick the same pause mode as the root, which is Stop (they will stop processing). You can override it by changing this mode in the inspector.
To force your timer to always tick, change its pause mode to Process.
Any way to do this when the timer is created in a script?