Fix repository cache invalidation issue when project is recreated with an empty repo

To reproduce:

1. Create a project with some content
2. Rename the project
3. Create a new project with the same name.
4. Boom - 404.

After step 2, the branch and tag counts were not being cleared. This would
cause `repository.has_visible_content?` to erroneously return `true`
for the newly-created project.

Closes #13384