Try doing a "yum clean all". What do you get from "yum repolist"? You can probably disable the clearos-contribs repo anyway as it is not enabled by default in 6.x.
FWIW 6.x is end of life and has not had any updated for nearly a year now. Can I suggest upgrading to 7.x?
Have a look at the OpenVPN config file /etc/openvpn/clients.conf. In the short term moving everything across will work when you move it across, but what happens when you need a new user? the CA is in ClearOS so you will need to create his/her certificate there. Also at some point the server certificate will need to be regenerated (but not the CA) to get round what is current a warning in the connection log "WARNING: --ns-cert-type is DEPRECATED. Use --remote-cert-tls instead.". This will have to happen before the OpenVPN 2.5 client is released.
You need a rule each for tcp and udp. You cannot do a port rule without a protocol.
In general communication is initiated from a high port (aka unprivileged port), so >=1024. It follows, then, that for security reasons, it is valid to block replies to low ports <1024. The exception to this is ntp when using the ntp program, when communication is from and to port 123, so installing NTP gets this rule. Having said that, chronyd and ntpdate are from high ports and at some point we may switch to using chronyd as it is the upstream default. You could argue that a really basic rule could suffice not specifying ports, protocols or interfaces, but it is unlikely that the firewall will get that sort of review until ClearOS 8.
I can't remember the details but, DHCP is either from 67 to 68 or vice versa, so the related/established rules are covered by the INPUT rules.The outbound request is allowed automatically by OUTPUT rules.
The ClearOS firewall does some odd things where it creates an OUTPUT rule for every INPUT rule it creates. This is generally unnecessary because of the related/established rules, but **may** be necessary for the FORWARD chain if the default policy is to block all and allow by exception. There has been an issue for this for years but as the firewall works, no one has bothered fixing it.
I checked my iptables rules and I don't understand some of the default rules,
1. Why the separate "RELATED,ESTABLISHED" rules? why not 1 for each interface to cover all ports?
2. for INPUT there are no "RELATED,ESTABLISHED" rules below port 1024, how does this work?
Why do we need DHCP port open on the WAN interface?
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I wish I was a Linux/ClearOS programmer and knew a lot more about the system layout and I would tackle it. In any event, thanks Nick! I do know there are a lot of good feature requests in the queue and all good things come in time. Most everything has a work around!
The webroot does not get redirected to /var/flexshare/shares. There are two different views of the same files. The only issue I know is that the CGI ScriptAlias points to the flexshare rather than directly to the path under /var/www, and someone reported an issue because of it.