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Why did changing my shell to fish break PATH in Gnome Shell?

I've recently added some tools and applications that I want to run in ~/.local/bin, as part of this process I installed fish and changed it to be my default shell. Everything was going well, I could run these tools from the terminal without having to specify the path, and the PATH variable was showing ~/.local/bin as being included. The .desktop files I had setup in ~/.local/share/applications also worked great.

I then restarted, suddenly ~/.local/bin is not in my PATH and nothing works as it did previously.

I then configured fish to update the path automatically like so:

set -U fish_user_paths ~/.local/bin $fish_user_paths

This allowed me to run my tools from the terminal, however the .desktop files still won't work.

Is it possible to configure my environment on login to set the path for both fish and gnome? Bash should already work as it's configured by default in ~/.bash_profile.