The problem is about this code snippet: pkg_preinst() { declare MOZILLA_FIVE_HOME=/usr/$(get_libdir)/${PN} echo "" elog "Removing old installs though some really ugly code. It potentially" elog "eliminates any problems during the install, however suggestions to" elog "replace this are highly welcome. Send comments and suggestions to" elog "mozilla@gentoo.org" rm -rf ${ROOT}${MOZILLA_FIVE_HOME} echo "" } Which was supposed to workaround some problems like bug 27719. But there is one annoying thing about it: all extension installed by portage are removed and you have to re-emerge them after updating thunderbird. Example: # Warn user that remerging enigmail is neccessary on USE=crypt use crypt && ewarn "Please remerge x11-plugins/enigmail after updating mozilla-thunderbird." I suggest to not remove the extensions directory in this remove-all phase. On my amd64 system it's /usr/lib64/mozilla-thunderbird/extensions, and I suppose it can be abstracted using get_libdir and/or MOZILLA_FIVE_HOME or something similar. In this bug report I assume that not removing the extensions dir won't affect build and installation and it will remove an annoying need to re-emerge extensions installed via portage (example: enigmail).
You need to reemerge the extensions, whether you want it or not. The extensions thing doesn't work only having a extension in it's dir. You need to install it again. Closing as CANTFIX, since we can't fix this.