Yes, the symlink is in place:

ls /etc/NetworkManager/system-connections
131205 lrwxrwxrwx 1 root root 32 Oct 17 21:17 
/etc/NetworkManager/system-connections -> /rw/config/NM-system-connections/


The /dev/xvdb is properly mounted on /rw :

/dev/xvdb on /rw type ext4 (rw,relatime,discard,data=ordered)
 
I don't have a /etc/system directory on my system, are you referring to the 
unit files?
For the sys-firewall I'm using the default template - > fedora-23

When I set the routes by hand via NetworkManager they are reflected on the 
qubes-uplink-eth0 file:
(...)
[ipv4]
address1=10.137.1.8/32,10.137.1.1
dns=10.137.1.1;10.137.1.254;
dns-search=
may-fail=false
method=manual
never-default=true
route1=192.168.0.0/16,10.137.1.1
route2=172.16.0.0/16,10.137.1.1
#---EOF---
 
The file before the sys-firewall is rebooted has the following checksum and 
md5sum:

2551335477 425 qubes-uplink-eth0
83b37a6b68007838efb1e9e9fbc841f4  qubes-uplink-eth0

As soon as the sys-firewall  is booted the file with the NW configuration is 
overwritten :

[ipv4]
method=manual
may-fail=false
dns=10.137.1.1;10.137.1.254
addresses1=10.137.1.8;32;10.137.1.1
#---EOF---

As you can see the configuration was not preserved.
Therefore something is clearly overwritten the NM configuration, the problem is 
to know what and how to avoid it, preserving the NM config.


So in short, I cannot tell what process have been changing the NM configuration 
at every boot. It would be great if someone from the Qubes support would be 
able to shed some light on this.





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