1. A computer-implemented method comprising: receiving a request to generate implicit dependencies introduced by runtime configuration files in a project; identifying, in the project, a source software element that references a runtime configuration file, wherein the runtime configuration file specifies a target function that is invoked at runtime; identifying, in the project, an invocation that references the runtime configuration file, wherein the invocation occurs in a source software element of the project; identifying, in the project, a definition of the target function referenced by the runtime configuration file, wherein the target function is defined in a target software element of the project; generating a new dependency in a raw dependency graph, the new dependency representing an implicit dependency from the source software element to the target software element; and generating, in an aggregated dependency graph that is different from the raw dependency graph, an aggregated dependency representing the implicit dependency from the source software element to the target software element.