CI in apache userdirs (domain.com/~user/public/ci)

I don't think the solution is in Paths.php. Nothing about the framework structure is being changed and components not found, just the install location. The Paths.php entries are all relative system paths and they are all still correct. Meanwhile, the 404 I'm getting is the CI-generated 404 page. So the framework is being located by apache ok, bootstrapped, and launched without issue.