After creating the two clones, as David Deutsch proposed, I recommend selecting it as the primary one and creating a symbolic link to the .idea directory from the secondary clone to the primary clone. This way you will have the same configuration in all clones.
ln -s primary_clone/.idea secondary_clone/.idea
It is assumed that you are using the .idea project configuration format and that you are not checking the configuration in the repository (in this case, you are obviously all configured from get go)
it works mostly, only sometimes Idea offers you a dialog box for reloading other projects if you change some settings in the current active one. However, you can refuse.
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