Fix root paths to be relative to project root

What does this MR do?

Fix the root paths so that their relative to the project root path. This is important as it is how linking between vulnerability and the file works in the UI.

What are the relevant issue numbers?

gitlab-org/gitlab#299585 (closed)

Does this MR meet the acceptance criteria?

• Changelog entry added
• Tests added for this feature/bug
• Conforms to the code review guidelines
• Conforms to the Go guidelines
• Security reports checked/validated by reviewer