See bug 1207335 for background. The p11-kit-trust module, should be able to easily distinguish between systemwide installed CAs that have their origin in the Mozilla/NSS CA list, from other systemwide installed CAs (which have been installed by the administrator, or as part of an deployment) The suggestion is to use filenames that start with "mozilla-nss-" for all such CA files. (It seems unlikely, but if there'll ever be a good reason to include CAs from other sources as trusted in the ca-certificates packages, those should use different filename prefixes.)
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