I had an existing wildfire 2.6.2 install. The update to 3.0.0 overwrote the contents of /opt/wildfire/resources/security/keystore and /opt/wildfire/resources/security/truststore with the default files from the distribution.
The ebuild add a line creating a env.d file that protects that directory: #Protect ssl key on upgrade echo 'CONFIG_PROTECT="/opt/wildfire/resources/security/"' > ${D}/etc/env.d/98wildfire But the file is not being created probably because ${D}/etc/env.d/ does not exist. I'll fix this tomorow morning.
I'm adding a revision to portage that fixes this issue and also that does a check for the env.d entry and that will pause asking the user to stop in case of upgrade.