Unfortunately, you will have a problem when you use a private CVS repository for your site, previously imported 4.6.3, and now import and merge 5.0. There are a number of packages which have been removed from the distribution tarball since 4.6.3, and merging the changes between 4.6.3 and 5.0 will cause these packages to disappear.
I only noticed this after doing the merge, and had to fix it by installing them from the "OpenACS Repository" on /acs-admin/install/, and adding them to my CVS repository again.
The upgrade instructions should mention this, with a list of packages that have been removed.
