How do you update a Makefile?



I'm basically a summer student working on a program called Rivet.
(http://projects.hepforge.org/rivet/) And I'm trying to port it to
BOINC so that the hosts can download the BOINC client and do some
calculation over a large clusters of computers.

Me being an absolute beginner at programming, I don't know how to
update the Makefile in Rivet! I edited the Makefile.am in the src
directory to include the BOINC APIs and Libraries, but what do you do
then? do you use autoconf to generate a Makefile.in? and then run ./
configure all overagain? cause if thats the case it didn't work.

Any help would be much appreciated!
Thanks
Chris
.



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