Systems and methods of executing and/or provisioning an application in an application specific runtime environment or general runtime environment are disclosed. The application specific runtime environment or general runtime environment are optionally defined by an application environment specification to include a minimal or reduced set of software resources required for execution of the application. These software resources are optionally stored in a resource repository that includes resources associated with a plurality of operating systems and/or executable applications. Various embodiments of the invention include the development of hierarchical resource metadata configured to characterize the various files, packages and file families included in the resource repository. In some embodiments this metadata is used to select between files when provisioning an application specific runtime environment. Various embodiments of the invention include use of an exclusion list to manage conflicts between same named files.