Just rewriting css and js tags and removing base tag would leave all the images broken. all told, there are HUNDREDS of these items. It's an enormous task. Additionally, the development directory is a subdirectory of the webroot. When a development scrum is over, files are published from the dev subfolder to the parent folder. This was the original motivation for the relative file references. It could be solved by using a var or constant in front of every single image, css, and js file, but this results in very nasty looking code.
I have managed to get the problem solved by using a relative path to the current document in the anchor tags:
<a href="some/file/fragment/file.php#anchor">LINK</a>
If I use a relative file reference, it doesn't force the page to reload. bizarre.