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When unrooted certificates are encountered, and the user is prompted and indicates to trust them, the CertificateChecker tries to save them to the trust engine, but that's generally read-only and then the trusted certificates are simply not remembered. Hence these same certificates are prompted again the next time. It would be better if, like PGP keys, they were stored in the profile preferences in the case they can't be stored in the trust engine. The Trust preference page could manage both certificates and keys just as the Trust dialog prompt already presents both in a unified way.
New Gerrit change created: https://git.eclipse.org/r/c/equinox/rt.equinox.p2/+/190615
Gerrit change https://git.eclipse.org/r/c/equinox/rt.equinox.p2/+/190615 was merged to [master]. Commit: http://git.eclipse.org/c/equinox/rt.equinox.p2.git/commit/?id=93851ec7fd3e76d5ccfa2fc6407353c3302c5e16