1. A system configured to control run-time implementation of an application by modification, addition, and/or removal of machine-readable instructions; the system comprising: one or more physical computer processors configured by computer readable instructions to: obtain machine-readable instructions that, when executed, cause a target computing platform to implement the application, the machine-readable instructions comprising instruction modules correspond to features of the application; obtain implementation information characterizing implementation of the application by the target computing platform; analyze the machine-readable instructions, instruction modules, and/or the implementation information; create rules that programmatically govern code addition, replacement, and/or modifications to modify features of the application, such creation of the rules being based on the analysis; obtain an implementation modification to effectuate in the application on the target computing platform; modify the machine-readable instructions to effectuate the implementation modification, such modification of the machine-readable instructions effectuating one or more of a modification of a feature of the application, an addition of a feature to the application, and/or a removal of a feature from the application, and such modification of the machine-readable instructions being determined based on the rules; and distribute the modified machine-readable instructions to the target computing platform to effectuate implementation by the target computing platform of the application with the implementation modification.