Description of problem:
When updating atomic RPMs package by rpm -Uvh, the /etc/containers/ will be removed from RHELAH, it will cause many issues such as failure to pull images by atomic(skopeo copy).

Version-Release number of selected component (if applicable):

[root@atomic-host-001 cloud-user]# cat /etc/redhat-release 
Red Hat Enterprise Linux Atomic Host release 7.3

[root@atomic-host-001 cloud-user]# atomic host status
State: idle
Deployments:
● rhel-atomic-host:rhel-atomic-host/7/x86_64/standard
       Version: 7.3 (2016-10-26 14:24:09)
        Commit: 90c9735becfff1c55c8586ae0f2c904bc0928f042cd4d016e9e0e2edd16e5e97
        OSName: rhel-atomic-host
  GPGSignature: (unsigned)
      Unlocked: development

[root@atomic-host-001 cloud-user]# rpm -q atomic docker skopeo
atomic-1.12.5-2.el7.x86_64
docker-1.10.3-57.el7.x86_64
skopeo-0.1.14-0.6.el7.x86_64

How reproducible:
always

Steps to Reproduce:
1. deploy rhel-atomic-cloud-7.3.0-3.x86_64 image in virtual environment and start it
2. download latest skopeo and atomic PRMs packages from brew system
3. rpm -Uvh skopeo* atomic*

Actual results:

[root@atomic-host-001 cloud-user]# ls /etc/containers/
policy.json  registries.d

[root@atomic-host-001 cloud-user]# ls /etc/containers/registries.d/
default.yaml

[root@atomic-host-001 cloud-user]# rpm -Uvh skopeo-0.1.17-0.5.git1f655f3.el7.x86_64.rpm 
Preparing...                          ################################# [100%]
Updating / installing...
   1:skopeo-1:0.1.17-0.5.git1f655f3.el################################# [ 50%]
Cleaning up / removing...
   2:skopeo-1:0.1.14-0.6.el7          ################################# [100%]

[root@atomic-host-001 cloud-user]# ls /etc/containers/
registries.d

NOTE: the /etc/containers/policy.json file is deleted after updating skopeo,
the subsequent atomic pull(skopeo copy) will try to open the file. 
 
[root@atomic-host-001 cloud-user]# rpm -Uvh atomic-1.13.7-2.el7.x86_64.rpm 
Preparing...                          ################################# [100%]
Updating / installing...
   1:atomic-1:1.13.7-2.el7            ################################# [ 50%]
Cleaning up / removing...
   2:atomic-1:1.12.5-2.el7            ################################# [100%]

[root@atomic-host-001 cloud-user]# ls /etc/containers/
ls: cannot access /etc/containers/: No such file or directory

NOTE: the whole /etc/containers/ is deleted after updating atomic. 

Expected results:

We should fix it in 7.3.1

Additional info:

Please also see bug 1381736