Reconfigurable transistors are a new emerging type of device, which offer the promise to improve the resistance of electronic components against know-how theft. In order to enable a product development of such an emerging device, a cross-layer design enablement strategy is needed, as emerging technologies are not necessarily compatible withstandard tools used in the industry. In 'CirroStrato', we aim on the development of such a complete flow enabling CMOS co-integration of reconfigurable transistors, ranging from process adjustments, device modeling, library characterization, physical and logical synthesis up towards sophisticated hardware security tests. In this multi-partner-project (MPP) paper, our aim is to elucidate the overall design enablement flow, as well as current research challenges on the individual stages.