repo: Port -refs.c to openat()

I'd like to incrementally convert all of `ostree-repo*.c` to
fd-relative usage, so that we can sanely introduce
`ostree_repo_new_at()` which doesn't involve GFile.

This one is medium risk, but passes the test suite.

tests/admin-test.sh

@@ -155,6 +155,8 @@ assert_not_streq ${rev} ${newrev}
 assert_file_has_content sysroot/ostree/deploy/testos/deploy/${newrev}.0/etc/os-release 'NAME=TestOS'
 ${CMD_PREFIX} ostree admin status
 validate_bootloader
+${CMD_PREFIX} ostree --repo=sysroot/ostree/repo refs testos:testos > reftest.txt
+assert_file_has_content reftest.txt testos:buildmaster/x86_64-runtime
 
 echo "ok upgrade"