As mentioned before, never, ever, modify wordpress core files. It is a maintenance nightmare and a security risk, and very, very bad practice.
During development the only area you need concern yourself with is the wp-content folder, specifically plugins and themes. Put post type registrations, url rewrites, custom taxonomies etc in a plugin, and visuals in themes.
Assuming you have svn or git as your version control, I would give wordpress_base its own repository. Then give each project a repo, containing the project folder, and an SVN External/Git submodule, that pulls in the base wordpress theme.
This way each project has its own repository, and its own history, but all share the wordpress_base folder, which is tracked separately and automatically pulled in via version control.
Also have you considered wordpress child themes instead of your Ant script?
Also if you’re working with Git, you can add an autodeployment script that puts a copy of the repos latest files from a branch in your live folder when you push commits to that branch on to the server.