Assuming your changes aren't exactly the same as the core
patches, you need to back out your changes before bringing in
the new core. To be able to do this cleanly, those changes need
to have been committed seperately to anything else (such as
changes in core to support your application, which you'll want to
What you need to do is find out which commits of which files are
the stuff you need to back out, get CVS to produce a suitable
patch, then apply it.
For example, you've made a bunch of changes to
foo.tcl, some of which are bugfixes (which you
now want to back out) and some of which are in support of your
application (which you want to keep).
cvs log foo.tcl shows you that
foo.tcl is at revision 1.9, and the list of commit
messages shows that 1.4 commit is the one you want to
cvs diff -r1.4 -r1.3 foo.tcl will give you a
patch that takes the code from 1.4 to 1.3, which if nothing since
has touched those lines will back out whatever change you've
made. Apply that patch, repeat for other modified files, then
you're set to import the updated core.