Given a CA certificate file 'foo.crt', follow these steps to install it on Debian

Copy your certificate /usr/local/share/ca-certificates/

and then, update certificate store:

update-ca-certificates

You should get this output:

Updating certificates in /etc/ssl/certs... 1 added, 0 removed; done.
Running hooks in /etc/ca-certificates/update.d....
Adding debian:foo.pem
done.
done.