Yes, they are.  For example, when I copied my local CA into /usr/share
/ca-certificates/mit.edu/mitCA.crt and ran `dpkg-reconfigure ca-
certificates`, it prompted me to activate them by checking a box.  This
caused the line ‘mit.edu/mitCA.crt’ to be added to ca-certificates.conf,
and so update-ca-certificates symlinked mitCA.pem into /etc/ssl/certs,
etc.

The problem is that, if all of this happens _before_ ca-certificates-
java is installed, then the ca-certificates-java postinst script never
takes any action on the added lines.  All the postinst does is remove
the CA that are marked with ‘!’ in ca-certificates.conf; it never adds
anything.  Therefore, the keystore stays out of sync (until I do
something like remove and re-add the certificate).

-- 
Keystore is not generated during package installation
https://bugs.launchpad.net/bugs/244410
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