Using robots to harvest sweet peppers in protected cropping environments has remained unsolved despite considerable effort by the research community over several decades. In this paper, we present the robotic harvester, Harvey, designed for sweet peppers in protected cropping environments that achieved a 76.5% success rate (within a modified scenario) which improves upon our prior work which achieved 58% and related sweet pepper harvesting work which achieved 33\%. This improvement was primarily achieved through the introduction of a novel peduncle segmentation system using an efficient deep convolutional neural network, in conjunction with 3D post-filtering to detect the critical cutting location. We benchmark the peduncle segmentation against prior art demonstrating a considerable improvement in performance with an F_1 score of 0.564 compared to 0.302. The robotic harvester uses a perception pipeline to detect a target sweet pepper and an appropriate grasp and cutting pose used to determine the trajectory of a multi-modal harvesting tool to grasp the sweet pepper and cut it from the plant. A novel decoupling mechanism enables the gripping and cutting operations to be performed independently. We perform an in-depth analysis of the full robotic harvesting system to highlight bottlenecks and failure points that future work could address.