Methods, systems, and apparatus, including computer programs encoded on computer storage media, for classifying system-generated code. One of the methods includes generating data representing a state of source code files of the snapshot before performing a build process for the snapshot. An instrumented build process is performed for the snapshot, including intercepting each compiler call of a plurality of compiler calls by the build process for the snapshot, and designating one or more respective source code files of each compiler call as source code files compiled during the build process for the snapshot. One or more source code files that are new or were modified after the build process was initiated are classified as source code files having system-generated source code.