Exploring architectures for large, modern FPGAs requires sophisticated software that can model and target hypothetical devices. Furthermore, research into new CAD algorithms often requires a complete and open source baseline CAD flow. This article describes recent advances in the open source Verilog-to-Routing (VTR) CAD flow that enable further research in these areas. VTR now supports designs with multiple clocks in both timing analysis and optimization. Hard adder/carry logic can be included in an architecture in various ways and significantly improves the performance of arithmetic circuits. The flow now models energy consumption, an increasingly important concern. The speed and quality of the packing algorithms have been significantly improved. VTR can now generate a netlist of the final post-routed circuit which enables detailed simulation of a design for a variety of purposes. We also release new FPGA architecture files and models that are much closer to modern commercial architectures, enabling more realistic experiments. Finally, we show that while this version of VTR supports new and complex features, it has a 1.5× compile time speed-up for simple architectures and a 6× speed-up for complex architectures compared to the previous release, with no degradation to timing or wire-length quality.