upgrade: fix handling of `.d` data file
The test did not used any `.d` file. So of course, their handling was broken
(for vfs encoding reason again). We fix the issue and update the test.
Note that some fncache issue remains with `.d` file. It will be taken care of
in the next changesets.
Differential Revision: https://phab.mercurial-scm.org/D6904