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Implement an "upgrade" capability for the key store file, and then use it to delete the old file. The existing certs in the old file are not a security risk, but they are now useless because the format of their aliases was changed in commit a4440b4. They now are just taking up storage space and memory. Users will need to re-accept *ALL* certificates that they had previously accepted and are still using. (Actually, this requirement was effective with commit 4b57d79a. Before that, certificates whose Subject matched did not require re-accepting.)