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 the 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 of the source software element on the target software element due to the source software element referencing the runtime configuration file specifying the target function defined in the target software element; and generating data representing an aggregated dependency graph for a plurality of nodes of a hierarchy graph of software elements in the project, the plurality of nodes comprising a first node and a second node, wherein the aggregated dependency graph is different from the raw dependency graph, including generating an aggregated dependency between the first node in the hierarchy graph and the second node in the hierarchy graph, the aggregated dependency representing the implicit dependency in the raw dependency graph of the source software element on the target software element, wherein the first node or a descendent of the first node in the hierarchy graph represents the source software element, and wherein the second node or a descendent of the second node in the hierarchy graph represents the target software element.