1. A non-transitory computer accessible storage medium storing a plurality of instructions which, when executed: read, from one or more files, a plurality of commands describing structural changes to be made to a hardware description language (HDL) representation of a circuit to produce a modified version of the HDL representation of the circuit for implementation on a programmable logic device (PLD); process the plurality of commands to cause the structural changes to be performed by automatically modifying HDL code in the HDL representation of the circuit, thereby producing the modified version of the HDL representation of the circuit, and store the modified version of the HDL representation of the circuit, including the modified HDL code, wherein a programmable logic device design tool is executable to receive the modified version of the HDL representation of the circuit and generate a bitstream for implementing the circuit on the PLD.