In Debian the standard SSL cert directory is /etc/ssl/certs. Certs whose hash is symlinked here (format: XXXXXXXX.n | X in hex, n in N) will be found system-wide. When a look-up for a domain is done, then this domain is hashed in the same way to determine the file the corresponding certificate will be found in. This global installation will allow for all applications to access the information and calculate trust chains.
If you install certificates to your browser only other applications like a web-server of vpn-client can not benefit from the installation.
The line below shows how to create a correct link.
ln -s newcert.pem $(openssl x509 -hash -noout -in newcert.pem).0