Bernhard R. Link ha wrote:

> The easiest way to make sure you have removed anything generated, is
> unpacking the source package, building it, then creating the source
> package and looking at the diff. As you use debian/patches for all your
> changes, the diff (best look at it with diffstat) should only contain
> files in the debian dir.

I don't know if this is a good and elegant solution, but I run 
aclocal,automake,autoconf
and I created a diff in debian/patches/ . In this way, make doesn't run again
aclocal,automake,autoconf and debian/rules clean  seems to work now...
I also changed version from 3.6~dfsg-1 to 3.6+dfsg-1 and uploaded to mentors:

- dget 
http://mentors.debian.net/debian/pool/main/f/freemat/freemat_3.6+dfsg-1.dsc


Giuseppe

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