Relative few tools and models with a specific focus on agroforestry are open source.
Two specific models that is Open Source are DynACof and the SHAMBA model.
On the tool side, no agroforestry specific open source tools exist. Many use QGIS to plan agroforestry systems and a few farmers to farmOS to manage their farms, though both have a broader focus.
The European digitAF project is working on enabling a more open and collaborative ecosystem for agroforestry tools and models, which also includes the development and transition to more open source tools and models.