Using the Tor included in TBB does not seem like a good idea. Once I changed settings on torrc, it began to look for files and directories that are expected in a full installation of Tor (.tor in home directory for example). Perhaps with symlinks it would be possible to get it to a usable state, but it might be prone to break.

As to the part about Tor Browser, it is not relevant. The idea is to make Tor transparent to every program. This way the program does not necessarily have to be SOCKS enabled to use Tor. Yes, I am aware that many programs could send sensitive information. This is a very stripped down box, so I'm not too worried about that.

I installed the version of Tor in the Trisquel repos just to experiment. It is unable to understand the setting "VirtualAddrNetworkIPv4" but "VirtualAddrNetwork" works. I was unable to get this to work with the sample rules provided on the wiki. The transproxy.firewall.sh script by isislovecruft does work however. It seems it should support multiple users, but no matter how I've tried I've been unable to get that working either. Also of note is that if I run it with just "root" as user, no program that I open from terminal using sudo is able to connect to the Internet. If, however, I give my user account access, using sudo results in the programs having Internet access. What does sudo do exactly?

If running NetworkManager, it is necessary to specify 127.0.0.1 as DNS right in the configuration here. It seems like NetworkManager ignores resolv.conf.

Also worth noting, that I have to restart Tor every time after booting up, otherwise I'm unable to connect after adding the iptables rules.

I'll look through that script to see if I can figure out how come it works and the sample rules on that wiki do not.

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