It may have hurt in the case of IFTTT but if we assume the OP is right then this would simply be an edge case. Just because it hurt one 3rd party using the API doesn't mean all third parties will be prevented from innovating. Assuming Twitter is creating API usage rules to steer developers more toward building a platform rather than just replicating Twitter's functionality (which is what most 3rd parties are doing, the OP is right) its just not feasible or a productive use of time to verify that any given app isn't reproducing functinality (hence why they even have rules to begin with).
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It may have hurt in the case of IFTTT but if we assume the OP is right then this would simply be an edge case. Just because it hurt one 3rd party using the API doesn't mean all third parties will be prevented from innovating. Assuming Twitter is creating API usage rules to steer developers more toward building a platform rather than just replicating Twitter's functionality (which is what most 3rd parties are doing, the OP is right) its just not feasible or a productive use of time to verify that any given app isn't reproducing functinality (hence why they even have rules to begin with).