Configuration flexibility and deadlock-free operation are two important goals of control research in flexible manufacturing systems. Configuration flexibility, the ability to quickly change manufacturing system components and their logical relationships to meet new production needs, requires automatic generation of control executables from high level system specifications. These control executables must guarantee deadlock-free operation. The resource order policy and the resource upstream neighborhood policy are configurable control policies that provide the deadlock-free guarantee. Each uses an ordering of system machines along with routing information to generate a set of configuration specific linear constraints. These constraints encode the system state (the distribution of job instances in the system) along with a buffer capacity function. A job instance can move forward in its route only if the resulting state satisfies the constraint set. These policies are correct since they guarantee deadlock-free operation, configurable since operating constraints are generated from high level system specifications, and scalable because the amount of computation required for policy setup and execution remains tractable with increasing system configuration size.