There are a bunch of autotools generated files which
are present on the CVS and which should not.
In the top directory, you should remove :
Only configure.in and Makefile.am should remain.
In all the sbdirectories, you should remove the Makefile.in
Now when somebody checkout the cvs he will regenerate
properly all those file which will then correspond to
his system/architecture by launching autoconf/automake
An easy and commonly used way to do that is to include
the script autogen.sh (attached) in you top directory.
Before you add it to the CVS, do not forget to check
that it has execution rigths enabled.