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
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