Won't work in Whonix 13. You need to wait for Whonix 14.
Connecting to Tor before ZeroNet
User -> Tor -> ZeroNet -> Internet
Get ZeroNet's signing key. 
gpg --recv-keys "960F FF2D 6C14 5AA6 13E8 491B 5B63 BAE6 CB96 13AE"
Update your package lists.
sudo apt-get update
sudo apt-get install python-stem python-msgpack git
git clone https://github.com/HelloZeroNet/ZeroNet.git
Get into ZeroNet folder.
Check ZeroNet signature.
git log --show-signature
Start ZeroNet. - Does not work yet! 
./zeronet.py --tor always --fileserver_ip $(qubesdb-read /qubes-ip)
./zeronet.py --tor always --fileserver_ip 10.152.152.11
To reconfigure Tor Browser so you can access the local web interface, apply the following six steps.
TODO: Check with TBB series 7.0+ once it becomes stable. There are alpha series bug reports that it doesn't work https://forums.whonix.org/t/new-version-of-tbb-no-longer-accepts-foxyproxy-plugin/2565/32
cp /usr/share/usability-misc/tbb-foxyproxy/foxyproxy.xml /home/user/.tb/tor-browser/Browser/TorBrowser/Data/Browser/profile.default/
Step Two: Download and install the add-on:
Browser Settings ->
Search: "foxyproxy" ->
Install: FoxyProxy Standard
This is safe to do since all add-ons on Mozilla's servers are now signed and verified by FireFox 43+.
Step Three: Restart Tor Browser.
To reverse this and restore the default Tor Browser fingerprint its best to use a VM snapshot taken before installing the add-on. Re-downloading Tor Browser is another option in case no snapshot was taken. Alternatively FoxyProxy can be removed via
Note: Tor Browser will soon ship with sandboxing on an opt-in basis. Unfortunately the initial sandbox versions are incompatible with such configurations and must not be enabled.
Start Tor Browser.
Go to the ZeroNet web interface. Paste http://127.0.0.1:43110 into Tor Browser's url field and press enter.
Done. You can now use ZeroNet.
You won't be able to use the following specialized Tor mode, you won't be able to use
--tor alwaysin Whonix 13. It is because a newer version of control-port-filter-python will be required which will be available when Whonix 14 gets released.
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