1. A method of modifying application implementation by modification, addition, and/or removal of machine-readable instructions, the method being implemented in a computer system including one or more physical processors and storage media storing machine-readable instructions, the method comprising: obtaining machine-readable instructions that, when executed, cause a target computing platform to implement the application, the machine-readable instructions comprising instruction modules that correspond to features of the application; obtaining implementation information characterizing implementation of the application by the target computing platform; analyzing the machine-readable instructions, instruction modules, and/or the implementation information; creating an instruction store of instruction modules corresponding to the features of the application, the creation of the instruction store including identification of the instruction modules based on recognition of patterns of method calls and/or commands in the machine-readable instructions; creating 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; obtaining an implementation modification to effectuate in the run-time implementation; modifying 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 distributing 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.