Refresh flow should update structure and remove packages deleted from metadata

At the moment, Fusion does not delete existing packages that were removed from the metadata if no other packages have a new version.

Steps to reproduce

• Add multiple packages to metadata and run build.
• Remove one package from metadata, keeping the others at the same version.
• Run build again.
• Fusion finds nothing new to build and performs a refresh.
• The removed package is still present in the structure.