1. Install the custom certificates into a location other than /etc/ssl/certs. This prevents the system from overwriting the certificates.
2.
When you use applications, manually reference the certificates. In most applications, you can customize the certificate bundle or path when you verify SSL requests with cURL's --cacert CLI argument. See Publishing to an RStudio Connect Server with a Self-Signed or Untrusted SSL Certificate for one example of how to manually reference certificates.
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