Can't run update in Taranis

I have this problem now too.
> I'm using Taranis, and I can no longer update my computer. It was
> working fine until yesterday, and I haven't messed with anything that
> should cause it to break. Is there anything I can do about this? Is
> it a known problem?
>
> This is the message it displays:
>
> Could not download all repository indexes
>
> The repository may no longer be available or could not be contacted
> because of network problems. If available an older version of the
> failed index will be used. Otherwise the repository will be ignored.
> Check your network connection and ensure the repository address in the
> preferences is correct.
>
> Failed to fetch
> http://archive.trisquel.info/trisquel/dists/taranis/Release Unable to
> find expected entry universe/binary-i386/Packages in Meta-index file
> (malformed Release file?)
> Failed to fetch
> http://archive.trisquel.info/trisquel/dists/taranis-updates/Release
> Unable to find expected entry universe/binary-i386/Packages in
> Meta-index file (malformed Release file?)
> Failed to fetch
> http://archive.trisquel.info/trisquel/dists/taranis-security/Release
> Unable to find expected entry universe/binary-i386/Packages in
> Meta-index file (malformed Release file?)
> Some index files failed to download, they have been ignored, or old
> ones used instead.
>
>

Probably some server is down. Change to another repository (e.g. via Synaptic pacman) or wait a day or two.

I think you should modify /etc/apt/sources.list to have something like this:

deb ftp://archive.trisquel.info/trisquel/ taranis main
deb-src ftp://archive.trisquel.info/trisquel/ taranis main
deb ftp://archive.trisquel.info/trisquel/ taranis-updates main
deb-src ftp://archive.trisquel.info/trisquel/ taranis-updates main
deb ftp://archive.trisquel.info/trisquel/ taranis-security main
deb-src ftp://archive.trisquel.info/trisquel/ taranis-security main

Other users, including myself, have experienced before unexpected changes in sources.list on 3.5 making it impossible to use repositories.

I can't remember now whether the mysterious addition of "universe" to the sources.list was the issue on 3.5 (I think it was, though). In any case, from the "/Release" bit on your original sources I guess you first installed Taranis RC and then updated to 4.0/4.1. That might have messed with your sources. "Universe" is one of the repositories of Ubuntu, the one maintained by the community and without official Ubuntu support. The official one is "main". In Trisquel there is not now such a distinction and everything goes into one single repo ("main"). Perhaps on the RC they kept Ubuntu's original distinction.