On Tue, 13 Nov 2012 07:21:51 -0800 (PST)
Ugo <ugo.pa...@gmail.com> wrote:

> That's one of the ideas I came up in the first place, but sadly not 
> possible.
> The code has to change a little bit for each website, i.e : a payment 
> processor for example, a different module, etc...
> It's not 100% exactly the same website, it's just that they share the
> same code base.

Have one "upstream" branch, which has magento unmodified (or modified
by incorporating changes relevant for all the sites), then fork one
branch per each site off that upstream branch.  Customize the code in
whatever way you wish on each of these branches.

The next time a new version of magento comes out you check out the
upstream branch, roll out the new release, commit, then check out each
of the "downstream" branches in turn and merge that upstream branch.
A similar procedure is carried out if you fix a bug in the common code
(thus modifying the upstream branch).

-- 


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