This enhancement is based on a chat with Mike Wannamaker. Basically his team's build system pre-processes some of the metadata before deployment, in particular creating static resource archives from another location. Right now the only supported form of deployment pre-processing is the substitution rules which couldn't handle this type of situation. Consider allowing user-configured deployment pre-processing steps similar to how IDEA allows pre-build ant targets.
It's possible that retrieval post-processing before display in the directory diff tool might be necessary for symmetry.