Introduce parameter to include direct dependencies in CFF only

[sdruskat]

References in CFF are meant to record direct dependencies only (which themselves are responsible in turn to record their own direct deps, etc.).

While due to the architecture of Eclipse RCP apps, this is of little consequence for Hexatomic itself, the plugin should do this for deeper trees. This should probs be an optional parameter ignoreTransitive or similar, defaulting to true (to be in accordance w/ the software citation principles).