I'm sure you already knew this, but you'll need to update the cvs modules for the repository at the same time you're doing this - these files are explicitly named in there:
src-support -a src/.cvsignore src/COPYING src/COPYING.LIB src/COPYING.NEWLIB
src/COPYING.LIBGLOSS src/ChangeLog src/MAINTAINERS
src/Makefile.def src/Makefile.in src/Makefile.tpl src/README
src/README-maintainer-mode src/config src/config-ml.in
src/config.guess src/config.if src/config.sub src/configure
src/configure.in src/contrib src/etc src/gettext.m4 src/install-sh
src/libtool.m4 src/ltcf-c.sh src/ltcf-cxx.sh src/ltcf-gcj.sh
src/ltconfig src/ltmain.sh src/makefile.vms src/missing src/mkdep
src/mkinstalldirs src/move-if-change src/mpw-README
src/mpw-build.in src/mpw-config.in src/mpw-configure
src/mpw-install src/setup.com src/src-release src/symlink-tree
src/ylwrap