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Computer-aided cryptography is an active area of research that develops and applies formal, machine-checkable approaches to the design, analysis, and implementation of cryptography. We present a cross-cutting systematization of the computer-aided cryptography literature, focusing on three main areas: (i) design-level security (both symbolic security and computational security), (ii) functional correctness and efficiency, and (iii) implementation-level security (with a focus on digital side-channel resistance). In each area, we first clarify the role of computer-aided cryptography---how it can help and what the caveats are---in addressing current challenges. We next present a taxonomy of state-of-the-art tools, comparing their accuracy, scope, trustworthiness, and usability. Then, we highlight their main achievements, trade-offs, and research challenges. After covering the three main areas, we present two case studies. First, we study efforts in combining tools focused on different areas to consolidate the guarantees they can provide. Second, we distill the lessons learned from the computer-aided cryptography community's involvement in the TLS 1.3 standardization effort. Finally, we conclude with recommendations to paper authors, tool developers, and standardization bodies moving forward.