dir: Fix spurious permission denied errors

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Currently this error is happening on the eos3.9 dev branch of Endless
OS:

Nov 19 12:05:55 endless eos-updater-flatpak-installer[464]:
eos-updater-flatpak-installer: Couldn’t apply some flatpak update
actions for this boot: Error opening directory
'/root/.local/share/flatpak/app': Permission denied

The reason is that we have a check in flatpak_dir_list_unused_refs() to
check if the per-user installation exists and only try to list the refs
there if so, but the existence check falsely succeeds due to the systemd
sandboxing on eos-updater-flatpak-installer.service, and
flatpak_dir_list_refs() then fails in find_used_refs(). Specifically the
ProtectHome=yes systemd service option makes /root inaccessible, and due
to a bug in GLib[1] this makes g_file_query_exists() falsely return TRUE
for any paths under /root.

So, check for not found and permission denied errors rather than doing
an existence check, as we should be doing anyway to avoid a
time-of-check/time-of-use race, as explained in the
g_file_query_exists() documentation.

[1] https://gitlab.gnome.org/GNOME/glib/-/issues/1237

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