We should probably let one of the PT developers advise you on the best way to design a patch.
Honestly, I'm not sure what is the process for building the PT tools from the individual class files in the lib directory. It appears like the lib class files are appended together to form the PT tools, probably to make the tools more standalone and eliminate complications from @INC and so on.
But I know I've seen at least one occasion where the code under lib didn't match the code assembled into one of the tools under bin (in the same release of PT). As if the code in lib were newer, and slightly refactored relative to the code in the stable tool.