Skip archiving deleted files and delete them during restore

[mcornea]

Currently ostree admin config-diff captures deleted files which makes the tar command fail as the file doesn't exist. Updating it so that deleted files are skipped.

Example for this scenario is when chrony service is disabled in favor of ptp:

[root@sno core]# ostree admin config-diff | grep chrony
M    chrony.conf
D    systemd/system/multi-user.target.wants/chronyd.service
A    machine-config-daemon/orig/etc/chrony.conf.mcdorig

[omertuc]

But perhaps their deletion is something we'd like to preserve?

Can you add a TODO?

[mcornea]

But perhaps their deletion is something we'd like to preserve?

Can you add a TODO?

Sure, added.

[donpenney]

/lgtm