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I know that the root store is located at /etc/ssl/certs and can be updated with update-ca-certificates. But where does it get it's certificates from? And how do browsers interact with it which have their own root store. What's the priority ranking herer?

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Copy the certificates to the folder /usr/local/share/ca-certificates and make sure they end with the extension .crt. When you run update-ca-certificates it will do more than just update to /etc/ssl/certs, it will also create the java cacerts file (tested with openjdk 8).

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