line 41: dodir usr/bin should be dodir /usr/bin this causes the ebuild to try to move the apollo binary to /bin after compiling, which is a Bad Thing.
Oops, apparently, that was not enough to fix it. This is what I get for not testing my solution.
please reopen this bug when you have some more info/fixes/bugs for this
meanwhile the dodir error has been fixed in portage.