don't patch the licence files

You can find the rationale for this in the Debian Policy Manual:
"Packages distributed under the UCB BSD license, the Apache license (version 2.0), the Artistic license, the GNU GPL (version 2 or 3), the GNU LGPL (versions 2, 2.1, or 3), and the GNU FDL (versions 1.2 or 1.3) should refer to the corresponding files under /usr/share/common-licenses,[93] rather than quoting them in the copyright file."
http://www.debian.org/doc/debian-policy/ch-docs.html#s-copyrightfile
Does that answer your question?

Partly, as this does not tell me why the need to make them links instead of providing the original file in the first place. That debian doc page tells me the procedure, but does not explain the rationale behind it.

This is worse than I thought. You folks point to the GPL version 3 (/usr/share/common-licenses/GPL). Specto is licensed GPL version 2. I am aware of the "or later" clause, but this is violating the intent of the authors. And I have not had the permission to use the GPL v3 from my fellow specto devs.

To me, it's a pretty damn good argument why you should not patch software's licenses just for the fun of it.

By the way, this post was not intended to be a flame (altough it sounds as if I was angry), it's really because I don't understand the benefits of this approach (on the contrary, I see drawbacks: bugs cropping up as the result of such patches, and errors like the wrong license being used).

I do understand that this is a unfortunate situation.
But I think both issues you raised (1. the license being patched and 2. the link to the GPLv3) are too broad to be discussed in this bug. They are general questions concerning many packages including this one.
Maybe it's better if you ask those questions on a mailing list or in IRC. If you got a satisfactory answer, please post it here, so we can decide on how to proceed.
I'll set the bug status to incomplete until then.

FYI here are two links I found, maybe they can help you:
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=431109
http://www.debian.org/legal/licenses/

Jean-François, is there any progress on this issues?

No, the Specto MOTU package in karmic still points to the GPL v3.
As for asking the question on the debian mailing lists, I did not have
the time/inclination/courage to do it.

For me it's just a error when patching the package. It should point to /usr/share/common-licenses/GPL-2, not /usr/share/common-licenses/GPL which is a symlink to GPL-3 (the "default" GPL). Sometimes ago, /usr/share/common-licenses/GPL linked to GPL-2 because the GPL-3 didn't exist.
The debian/copyright should also be fixed by changing the link from GPL to GPL-2.

@Simon Do you want to prepare a fix for this ?

Julien, attached is a debdiff, that links to GPL-2 not GPL.

Jean-François, I think you should update the license of specto and remove the 'or later' part. This would make it clear that you intent to license specto under GPLv2.

This bug was fixed in the package specto - 0.3.1-0ubuntu2

---------------
specto (0.3.1-0ubuntu2) karmic; urgency=low

  [ Simon Olofsson ]
  * debian/copyright:
  * debian/patches/01_use_common_licenses.patch:
    + Link to GPL-2 not GPL (LP: #390240)

  [ Julien Lavergne ]
  * debian/control:
   - Remove useless depends on python-gnome2-extras.
   - Build specto only for python >= 2.5 (LP: #410693)

 -- Julien Lavergne <email address hidden> Sun, 30 Aug 2009 13:09:15 +0200