This paper proposes using file system custom metadata as a bidirectional communication channel between applications and the storage system. This channel can be used to pass hints that enable cross-layer optimizations, an option hindered today by the ossified file-system interface. We study this approach in context of storage system support for large-scale workflow execution systems: Our workflow optimized storage system (WOSS), exploits application hints to provide per-file optimized operations, and exposes data location to enable location-aware scheduling. This paper argues that an incremental adoption path for adopting cross-layer optimizations in storage systems exists, presents the system architecture for a workflow-optimized storage system and its integration with a workflow runtime engine, and evaluates the proposed approach using synthetic as well as real applications workloads.