Binary files in an executable file system can be directly executed by the central processing unit at the location in which the binary files are stored. A pre-runtime tool can traverse a replica directory hierarchy in a host/loading computer to fill an internal data structure which can be used to generate a binary file that can be loaded directly into the embedded computer. The central processing unit (CPU) and its components such as the address bus, data bus, and program counter, can directly interact with unit of storage interface mechanisms, such as read/write means, identifying location means, and concatenation means. In some embodiments, the page size in the memory management unit (MMU) of the CPU is set to the same size as the unit of storage.