This literature review surveys the extant research from 2018 through October 2022 in three key conferences related to software engineering and repository mining: Mining Software Repositories (MSR), the International Conference on Software Engineering (ICSE), and the International Conference on Software Maintenance and Evolution (ICSME). The review taxonifies hundreds of research papers, and provides summary and analysis of noteworthy papers related to code writing and refactoring, code comprehension, smells and code quality, aspects of software development related to an entire software project, and human dynamics within that project. The review also explores cross cutting themes among these topics, such as bots, machine learning, and the influence of different environments — such as free open source projects vs start ups vs established industry — on the development process. Underlying this work is an eye to research applicable to the advanced scientific computing space, which, in the United States, is often performed at national laboratories.